0s autopkgtest [16:53:47]: starting date and time: 2024-03-25 16:53:47+0000 0s autopkgtest [16:53:47]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:53:47]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tq3tbrxu/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 --apt-upgrade bowtie2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=perl/5.38.2-3.2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-arm64-9.secgroup --name adt-noble-arm64-bowtie2-20240325-165347-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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://ftpmaster.internal/ubuntu/ 194s autopkgtest [16:57:01]: testbed dpkg architecture: arm64 195s autopkgtest [16:57:02]: testbed apt version: 2.7.12 195s autopkgtest [16:57:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 196s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 197s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 198s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3992 kB] 200s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 200s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.8 kB] 200s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [713 kB] 200s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 200s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [39.7 kB] 200s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 200s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4354 kB] 201s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 201s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [71.0 kB] 201s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 209s Fetched 9860 kB in 6s (1588 kB/s) 210s Reading package lists... 216s Reading package lists... 216s Building dependency tree... 216s Reading state information... 218s Calculating upgrade... 219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 219s Reading package lists... 220s Building dependency tree... 220s Reading state information... 222s 0 upgraded, 0 newly installed, 0 to remove and 247 not upgraded. 224s sh: Attempting to set up Debian/Ubuntu apt sources automatically 224s sh: Distribution appears to be Ubuntu 227s Reading package lists... 227s Building dependency tree... 227s Reading state information... 229s eatmydata is already the newest version (131-1). 229s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 229s Reading package lists... 230s Building dependency tree... 230s Reading state information... 231s dbus is already the newest version (1.14.10-4ubuntu1). 231s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 231s Reading package lists... 232s Building dependency tree... 232s Reading state information... 234s rng-tools-debian is already the newest version (2.4). 234s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 234s Reading package lists... 234s Building dependency tree... 234s Reading state information... 236s The following packages will be REMOVED: 236s cloud-init* python3-configobj* python3-debconf* 237s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 237s After this operation, 3256 kB disk space will be freed. 237s (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 ... 75911 files and directories currently installed.) 237s Removing cloud-init (24.1.2-0ubuntu1) ... 240s Removing python3-configobj (5.0.8-3) ... 241s Removing python3-debconf (1.5.86) ... 241s Processing triggers for man-db (2.12.0-3) ... 242s (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 ... 75522 files and directories currently installed.) 242s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 245s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 245s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 245s invoke-rc.d: policy-rc.d denied execution of try-restart. 246s Reading package lists... 246s Building dependency tree... 246s Reading state information... 248s linux-generic is already the newest version (6.8.0-11.11+1). 248s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 248s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 249s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 249s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 258s Reading package lists... 258s Reading package lists... 258s Building dependency tree... 258s Reading state information... 260s Calculating upgrade... 261s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 261s Reading package lists... 262s Building dependency tree... 262s Reading state information... 263s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 264s autopkgtest [16:58:11]: rebooting testbed after setup commands that affected boot 429s autopkgtest [17:00:56]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 435s autopkgtest [17:01:02]: @@@@@@@@@@@@@@@@@@@@ apt-source bowtie2 441s Get:1 http://ftpmaster.internal/ubuntu noble/universe bowtie2 2.5.2-1 (dsc) [2513 B] 441s Get:2 http://ftpmaster.internal/ubuntu noble/universe bowtie2 2.5.2-1 (tar) [10.6 MB] 441s Get:3 http://ftpmaster.internal/ubuntu noble/universe bowtie2 2.5.2-1 (diff) [19.8 kB] 442s gpgv: Signature made Wed Jan 10 20:06:52 2024 UTC 442s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 442s gpgv: issuer "tillea@rki.de" 442s gpgv: Can't check signature: No public key 442s dpkg-source: warning: cannot verify inline signature for ./bowtie2_2.5.2-1.dsc: no acceptable signature found 443s autopkgtest [17:01:10]: testing package bowtie2 version 2.5.2-1 444s autopkgtest [17:01:11]: build not needed 464s autopkgtest [17:01:31]: test run-unit-test: preparing testbed 470s Reading package lists... 471s Building dependency tree... 471s Reading state information... 472s Starting pkgProblemResolver with broken count: 0 472s Starting 2 pkgProblemResolver with broken count: 0 472s Done 473s The following additional packages will be installed: 473s bowtie2 bowtie2-examples libclone-perl libconfig-general-perl 473s libfile-which-perl libmath-random-perl libsys-info-base-perl 473s libsys-info-driver-linux-perl libsys-info-perl libtest-deep-perl 473s libunix-processors-perl 473s The following NEW packages will be installed: 473s autopkgtest-satdep bowtie2 bowtie2-examples libclone-perl 473s libconfig-general-perl libfile-which-perl libmath-random-perl 473s libsys-info-base-perl libsys-info-driver-linux-perl libsys-info-perl 473s libtest-deep-perl libunix-processors-perl 473s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 473s Need to get 11.2 MB/11.2 MB of archives. 473s After this operation, 14.3 MB of additional disk space will be used. 473s Get:1 /tmp/autopkgtest.LtLaNF/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [764 B] 474s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libclone-perl arm64 0.46-1build1 [10.4 kB] 474s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libconfig-general-perl all 2.65-2 [57.1 kB] 474s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libfile-which-perl all 1.27-2 [12.5 kB] 474s Get:5 http://ftpmaster.internal/ubuntu noble/multiverse arm64 libmath-random-perl arm64 0.72-2build3 [48.9 kB] 474s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libsys-info-base-perl all 0.7807-4 [27.0 kB] 474s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libunix-processors-perl arm64 2.046-3build2 [15.3 kB] 474s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libsys-info-driver-linux-perl all 0.7905-6 [24.1 kB] 474s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libsys-info-perl all 0.7811-3 [6662 B] 474s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-deep-perl all 1.204-1 [47.1 kB] 474s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie2 arm64 2.5.2-1 [1261 kB] 474s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie2-examples all 2.5.2-1 [9707 kB] 480s Fetched 11.2 MB in 6s (1929 kB/s) 480s Selecting previously unselected package libclone-perl:arm64. 481s (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 ... 75467 files and directories currently installed.) 481s Preparing to unpack .../00-libclone-perl_0.46-1build1_arm64.deb ... 481s Unpacking libclone-perl:arm64 (0.46-1build1) ... 481s Selecting previously unselected package libconfig-general-perl. 481s Preparing to unpack .../01-libconfig-general-perl_2.65-2_all.deb ... 481s Unpacking libconfig-general-perl (2.65-2) ... 481s Selecting previously unselected package libfile-which-perl. 481s Preparing to unpack .../02-libfile-which-perl_1.27-2_all.deb ... 481s Unpacking libfile-which-perl (1.27-2) ... 481s Selecting previously unselected package libmath-random-perl. 481s Preparing to unpack .../03-libmath-random-perl_0.72-2build3_arm64.deb ... 481s Unpacking libmath-random-perl (0.72-2build3) ... 481s Selecting previously unselected package libsys-info-base-perl. 481s Preparing to unpack .../04-libsys-info-base-perl_0.7807-4_all.deb ... 481s Unpacking libsys-info-base-perl (0.7807-4) ... 481s Selecting previously unselected package libunix-processors-perl:arm64. 481s Preparing to unpack .../05-libunix-processors-perl_2.046-3build2_arm64.deb ... 481s Unpacking libunix-processors-perl:arm64 (2.046-3build2) ... 481s Selecting previously unselected package libsys-info-driver-linux-perl. 481s Preparing to unpack .../06-libsys-info-driver-linux-perl_0.7905-6_all.deb ... 481s Unpacking libsys-info-driver-linux-perl (0.7905-6) ... 481s Selecting previously unselected package libsys-info-perl. 481s Preparing to unpack .../07-libsys-info-perl_0.7811-3_all.deb ... 481s Unpacking libsys-info-perl (0.7811-3) ... 481s Selecting previously unselected package libtest-deep-perl. 482s Preparing to unpack .../08-libtest-deep-perl_1.204-1_all.deb ... 482s Unpacking libtest-deep-perl (1.204-1) ... 482s Selecting previously unselected package bowtie2. 482s Preparing to unpack .../09-bowtie2_2.5.2-1_arm64.deb ... 482s Unpacking bowtie2 (2.5.2-1) ... 482s Selecting previously unselected package bowtie2-examples. 482s Preparing to unpack .../10-bowtie2-examples_2.5.2-1_all.deb ... 482s Unpacking bowtie2-examples (2.5.2-1) ... 482s Selecting previously unselected package autopkgtest-satdep. 482s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 482s Unpacking autopkgtest-satdep (0) ... 482s Setting up libfile-which-perl (1.27-2) ... 482s Setting up libconfig-general-perl (2.65-2) ... 482s Setting up libtest-deep-perl (1.204-1) ... 482s Setting up libmath-random-perl (0.72-2build3) ... 482s Setting up libclone-perl:arm64 (0.46-1build1) ... 482s Setting up bowtie2 (2.5.2-1) ... 482s Setting up libunix-processors-perl:arm64 (2.046-3build2) ... 482s Setting up bowtie2-examples (2.5.2-1) ... 482s Setting up libsys-info-base-perl (0.7807-4) ... 482s Setting up libsys-info-driver-linux-perl (0.7905-6) ... 482s Setting up libsys-info-perl (0.7811-3) ... 482s Setting up autopkgtest-satdep (0) ... 482s Processing triggers for man-db (2.12.0-3) ... 491s (Reading database ... 75727 files and directories currently installed.) 491s Removing autopkgtest-satdep (0) ... 492s autopkgtest [17:01:59]: test run-unit-test: [----------------------- 493s \1 better written as $1 at simple_tests.pl line 4674. 493s \1 better written as $1 at simple_tests.pl line 4675. 494s FASTA-continuous 1 (fw:1, sam:1) 494s References: 494s >0 494s AGCATCGATCAGTATCTGA 494s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 494s /usr/bin/bowtie2 -F 10,9 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz 495s @HD VN:1.5 SO:unsorted GO:query 495s @SQ SN:0 LN:19 495s @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 6 -x .simple_tests.tmp .simple_tests.gz" 495s 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 495s 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 495s FASTA-continuous 2 (fw:1, sam:1) 495s References: 495s >0 495s AGCATCGATCAGTATCTGA 495s /usr/bin/bowtie2 -F 10,9 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz 495s @HD VN:1.5 SO:unsorted GO:query 495s @SQ SN:0 LN:19 495s @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 8 -x .simple_tests.tmp .simple_tests.gz" 495s 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 495s 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 495s 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 495s FASTA-continuous 3 (fw:1, sam:1) 495s References: 495s >0 495s AGCATCGATCAGTATCTGA 495s /usr/bin/bowtie2 -F 10,9 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz 495s @HD VN:1.5 SO:unsorted GO:query 495s @SQ SN:0 LN:19 495s @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 12 -x .simple_tests.tmp .simple_tests.gz" 495s 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 495s FASTA-continuous 4 (fw:1, sam:1) 495s References: 495s >0 495s AGCATCGATCAGTATCTGA 495s /usr/bin/bowtie2 -F 10,9 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz 495s @HD VN:1.5 SO:unsorted GO:query 495s @SQ SN:0 LN:19 495s @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 4 -x .simple_tests.tmp .simple_tests.gz" 495s 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 495s FASTA-continuous 5 (fw:1, sam:1) 495s References: 495s >0 495s AGCATCGATCAGTATCTGA 495s /usr/bin/bowtie2 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz 495s @HD VN:1.5 SO:unsorted GO:query 495s @SQ SN:0 LN:19 495s @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 7 -x .simple_tests.tmp .simple_tests.gz" 495s 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 495s FASTA-continuous 6 (fw:1, sam:1) 495s References: 495s >0 495s AGCATCGATCAG 495s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 496s /usr/bin/bowtie2 -F 10,1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz 496s @HD VN:1.5 SO:unsorted GO:query 496s @SQ SN:0 LN:12 496s @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 15 -x .simple_tests.tmp .simple_tests.gz" 496s 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 496s 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 496s 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 496s Align should not fail when first seq in ref is all Ns (fw:1, sam:1) 496s References: 496s >0 496s NNNNNNNNNNNNNNN 496s >1 496s AGCATCGATCAGTATCTGA 496s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 496s Warning: Encountered reference sequence with only gaps 497s Warning: Encountered reference sequence with only gaps 497s /usr/bin/bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG 497s @HD VN:1.5 SO:unsorted GO:query 497s @SQ SN:0 LN:15 497s @SQ SN:1 LN:19 497s @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 -c CATCGATCAGTATCTG" 497s 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 497s Align should not fail when multiple seqs are all Ns (fw:1, sam:1) 497s References: 497s >0 497s NNNNNNNNNNNNNNN 497s >1 497s NNNNNNNNNNNNNNN 497s >2 497s AGCATCGATCAGTATCTGA 497s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 497s Warning: Encountered reference sequence with only gaps 497s Warning: Encountered reference sequence with only gaps 498s Warning: Encountered reference sequence with only gaps 498s Warning: Encountered reference sequence with only gaps 498s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG 498s @HD VN:1.5 SO:unsorted GO:query 498s @SQ SN:0 LN:15 498s @SQ SN:1 LN:15 498s @SQ SN:2 LN:19 498s @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 -c CATCGATCAGTATCTG" 498s 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 498s Should account for stretch of Ns at beginning (fw:1, sam:1) 498s References: 498s >0 498s NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA 498s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 499s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG 499s @HD VN:1.5 SO:unsorted GO:query 499s @SQ SN:0 LN:34 499s @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" 499s 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 499s Cline 1 (fw:1, sam:1) 499s References: 499s >0 499s AGCATCGATCAGTATCTGA 499s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 500s /usr/bin/bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG 500s @HD VN:1.5 SO:unsorted GO:query 500s @SQ SN:0 LN:19 500s @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" 500s 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 500s Cline 2 (fw:1, sam:1) 500s References: 500s >0 500s AGCATCGATCAGTATCTGA 500s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 500s @HD VN:1.5 SO:unsorted GO:query 500s @SQ SN:0 LN:19 500s @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 -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 500s 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 500s Cline 2 (fw:1, sam:1) 500s References: 500s >0 500s AGCATCGATCAGTATCTGA 500s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP 500s @HD VN:1.5 SO:unsorted GO:query 500s @SQ SN:0 LN:19 500s @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:ABCDEDGHIJKLMNOP" 500s 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 500s Cline 4 (fw:1, sam:1) 500s References: 500s >0 500s AGCATCGATCAGTATCTGA 500s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO 501s Error: Read 0 has more read characters than quality values. 501s terminate called after throwing an instance of 'int' 502s Aborted (core dumped) 502s (ERR): bowtie2-align exited with value 134 502s Cline 5 (fw:1, sam:1) 502s References: 502s >0 502s AGCATCGATCAGTATCTGA 502s /usr/bin/bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ 502s Error: Read 0 has more quality values than read characters. 502s terminate called after throwing an instance of 'int' 502s Aborted (core dumped) 502s (ERR): bowtie2-align exited with value 134 502s trim-to: trim from 5'-end (fw:1, sam:1) 502s References: 502s >0 502s AGCATCGATCAGTATCTGA 502s /usr/bin/bowtie2 --trim-to 5:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 502s 502s @HD VN:1.5 SO:unsorted GO:query 502s @SQ SN:0 LN:19 502s @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 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 502s 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 502s trim-to: trim from 3'-end (fw:1, sam:1) 502s References: 502s >0 502s AGCATCGATCAGTATCTGA 502s /usr/bin/bowtie2 --trim-to 3:12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 502s 503s @HD VN:1.5 SO:unsorted GO:query 503s @SQ SN:0 LN:19 503s @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 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 503s 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 503s trim-to: trim from 3'-end (default) (fw:1, sam:1) 503s References: 503s >0 503s AGCATCGATCAGTATCTGA 503s /usr/bin/bowtie2 --trim-to 12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 503s 503s @HD VN:1.5 SO:unsorted GO:query 503s @SQ SN:0 LN:19 503s @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 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 503s 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 503s trim-to: invalid position (fw:1, sam:1) 503s References: 503s >0 503s AGCATCGATCAGTATCTGA 503s /usr/bin/bowtie2 --trim-to 4:12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 503s 503s --trim-to: trim position must be either 3 or 5 503s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 503s Usage: 503s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 503s 503s Index filename prefix (minus trailing .X.bt2). 503s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 503s Files with #1 mates, paired with files in . 503s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 503s Files with #2 mates, paired with files in . 503s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 503s Files with unpaired reads. 503s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 503s Files with interleaved paired-end FASTQ/FASTA reads 503s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 503s Files are unaligned BAM sorted by read name. 503s File for SAM output (default: stdout) 503s 503s , , can be comma-separated lists (no whitespace) and can be 503s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 503s 503s Options (defaults in parentheses): 503s 503s Input: 503s -q query input files are FASTQ .fq/.fastq (default) 503s --tab5 query input files are TAB5 .tab5 503s --tab6 query input files are TAB6 .tab6 503s --qseq query input files are in Illumina's qseq format 503s -f query input files are (multi-)FASTA .fa/.mfa 503s -r query input files are raw one-sequence-per-line 503s -F k:,i: query input files are continuous FASTA where reads 503s are substrings (k-mers) extracted from a FASTA file 503s and aligned at offsets 1, 1+i, 1+2i ... end of reference 503s -c , , are sequences themselves, not files 503s -s/--skip skip the first reads/pairs in the input (none) 503s -u/--upto stop after first reads/pairs (no limit) 503s -5/--trim5 trim bases from 5'/left end of reads (0) 503s -3/--trim3 trim bases from 3'/right end of reads (0) 503s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 503s If the read end is not specified then it defaults to 3 (0) 503s --phred33 qualities are Phred+33 (default) 503s --phred64 qualities are Phred+64 503s --int-quals qualities encoded as space-delimited integers 503s 503s Presets: Same as: 503s For --end-to-end: 503s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 503s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 503s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 503s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 503s 503s For --local: 503s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 503s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 503s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 503s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 503s 503s Alignment: 503s -N max # mismatches in seed alignment; can be 0 or 1 (0) 503s -L length of seed substrings; must be >3, <32 (22) 503s -i interval between seed substrings w/r/t read len (S,1,1.15) 503s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 503s --dpad include extra ref chars on sides of DP table (15) 503s --gbar disallow gaps within nucs of read extremes (4) 503s --ignore-quals treat all quality values as 30 on Phred scale (off) 503s --nofw do not align forward (original) version of read (off) 503s --norc do not align reverse-complement version of read (off) 503s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 503s scan for the optimal seeded alignments 503s --end-to-end entire read must align; no clipping (on) 503s OR 503s --local local alignment; ends might be soft clipped (off) 503s 503s Scoring: 503s --ma match bonus (0 for --end-to-end, 2 for --local) 503s --mp max penalty for mismatch; lower qual = lower penalty (6) 503s --np penalty for non-A/C/G/Ts in read/ref (1) 503s --rdg , read gap open, extend penalties (5,3) 503s --rfg , reference gap open, extend penalties (5,3) 503s --score-min min acceptable alignment score w/r/t read length 503s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 503s 503s Reporting: 503s (default) look for multiple alignments, report best, with MAPQ 503s OR 503s -k report up to alns per read; MAPQ not meaningful 503s OR 503s -a/--all report all alignments; very slow, MAPQ not meaningful 503s 503s Effort: 503s -D give up extending after failed extends in a row (15) 503s -R for reads w/ repetitive seeds, try sets of seeds (2) 503s 503s Paired-end: 503s -I/--minins minimum fragment length (0) 503s -X/--maxins maximum fragment length (500) 503s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 503s --no-mixed suppress unpaired alignments for paired reads 503s --no-discordant suppress discordant alignments for paired reads 503s --dovetail concordant when mates extend past each other 503s --no-contain not concordant when one mate alignment contains other 503s --no-overlap not concordant when mates overlap at all 503s 503s BAM: 503s --align-paired-reads 503s Bowtie2 will, by default, attempt to align unpaired BAM reads. 503s Use this option to align paired-end reads instead. 503s --preserve-tags Preserve tags from the original BAM record by 503s appending them to the end of the corresponding SAM output. 503s 503s Output: 503s -t/--time print wall-clock time taken by search phases 503s --un write unpaired reads that didn't align to 503s --al write unpaired reads that aligned at least once to 503s --un-conc write pairs that didn't align concordantly to 503s --al-conc write pairs that aligned concordantly at least once to 503s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 503s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 503s --quiet print nothing to stderr except serious errors 503s --met-file send metrics to file at (off) 503s --met-stderr send metrics to stderr (off) 503s --met report internal counters & metrics every secs (1) 503s --no-unal suppress SAM records for unaligned reads 503s --no-head suppress header lines, i.e. lines starting with @ 503s --no-sq suppress @SQ header lines 503s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 503s --rg add ("lab:value") to @RG line of SAM header. 503s Note: @RG line only printed when --rg-id is set. 503s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 503s --sam-no-qname-trunc 503s Suppress standard behavior of truncating readname at first whitespace 503s at the expense of generating non-standard SAM. 503s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 503s --soft-clipped-unmapped-tlen 503s Exclude soft-clipped bases when reporting TLEN 503s --sam-append-comment 503s Append FASTA/FASTQ comment to SAM record 503s 503s Performance: 503s -p/--threads number of alignment threads to launch (1) 503s --reorder force SAM output order to match order of input reads 503s --mm use memory-mapped I/O for index; many 'bowtie's can share 503s 503s Other: 503s --qc-filter filter out reads that are bad according to QSEQ filter 503s --seed seed for random number generator (0) 503s --non-deterministic 503s seed rand. gen. arbitrarily instead of using read attributes 503s --version print version information and quit 503s -h/--help print this usage message 503s Error: Encountered internal Bowtie 2 exception (#1) 503s Command: /usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 503s (ERR): bowtie2-align exited with value 1 503s trim-to: invalid count (fw:1, sam:1) 503s References: 503s >0 503s AGCATCGATCAGTATCTGA 503s /usr/bin/bowtie2 --trim-to 5:-12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 503s 503s --trim-to: the number bases to trim must be at least 0 503s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 503s Usage: 503s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 503s 503s Index filename prefix (minus trailing .X.bt2). 503s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 503s Files with #1 mates, paired with files in . 503s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 503s Files with #2 mates, paired with files in . 503s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 503s Files with unpaired reads. 503s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 503s Files with interleaved paired-end FASTQ/FASTA reads 503s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 503s Files are unaligned BAM sorted by read name. 503s File for SAM output (default: stdout) 503s 503s , , can be comma-separated lists (no whitespace) and can be 503s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 503s 503s Options (defaults in parentheses): 503s 503s Input: 503s -q query input files are FASTQ .fq/.fastq (default) 503s --tab5 query input files are TAB5 .tab5 503s --tab6 query input files are TAB6 .tab6 503s --qseq query input files are in Illumina's qseq format 503s -f query input files are (multi-)FASTA .fa/.mfa 503s -r query input files are raw one-sequence-per-line 503s -F k:,i: query input files are continuous FASTA where reads 503s are substrings (k-mers) extracted from a FASTA file 503s and aligned at offsets 1, 1+i, 1+2i ... end of reference 503s -c , , are sequences themselves, not files 503s -s/--skip skip the first reads/pairs in the input (none) 503s -u/--upto stop after first reads/pairs (no limit) 503s -5/--trim5 trim bases from 5'/left end of reads (0) 503s -3/--trim3 trim bases from 3'/right end of reads (0) 503s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 503s If the read end is not specified then it defaults to 3 (0) 503s --phred33 qualities are Phred+33 (default) 503s --phred64 qualities are Phred+64 503s --int-quals qualities encoded as space-delimited integers 503s 503s Presets: Same as: 503s For --end-to-end: 503s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 503s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 503s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 503s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 503s 503s For --local: 503s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 503s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 503s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 503s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 503s 503s Alignment: 503s -N max # mismatches in seed alignment; can be 0 or 1 (0) 503s -L length of seed substrings; must be >3, <32 (22) 503s -i interval between seed substrings w/r/t read len (S,1,1.15) 503s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 503s --dpad include extra ref chars on sides of DP table (15) 503s --gbar disallow gaps within nucs of read extremes (4) 503s --ignore-quals treat all quality values as 30 on Phred scale (off) 503s --nofw do not align forward (original) version of read (off) 503s --norc do not align reverse-complement version of read (off) 503s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 503s scan for the optimal seeded alignments 503s --end-to-end entire read must align; no clipping (on) 503s OR 503s --local local alignment; ends might be soft clipped (off) 503s 503s Scoring: 503s --ma match bonus (0 for --end-to-end, 2 for --local) 503s --mp max penalty for mismatch; lower qual = lower penalty (6) 503s --np penalty for non-A/C/G/Ts in read/ref (1) 503s --rdg , read gap open, extend penalties (5,3) 503s --rfg , reference gap open, extend penalties (5,3) 503s --score-min min acceptable alignment score w/r/t read length 503s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 503s 503s Reporting: 503s (default) look for multiple alignments, report best, with MAPQ 503s OR 503s -k report up to alns per read; MAPQ not meaningful 503s OR 503s -a/--all report all alignments; very slow, MAPQ not meaningful 503s 503s Effort: 503s -D give up extending after failed extends in a row (15) 503s -R for reads w/ repetitive seeds, try sets of seeds (2) 503s 503s Paired-end: 503s -I/--minins minimum fragment length (0) 503s -X/--maxins maximum fragment length (500) 503s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 503s --no-mixed suppress unpaired alignments for paired reads 503s --no-discordant suppress discordant alignments for paired reads 503s --dovetail concordant when mates extend past each other 503s --no-contain not concordant when one mate alignment contains other 503s --no-overlap not concordant when mates overlap at all 503s 503s BAM: 503s --align-paired-reads 503s Bowtie2 will, by default, attempt to align unpaired BAM reads. 503s Use this option to align paired-end reads instead. 503s --preserve-tags Preserve tags from the original BAM record by 503s appending them to the end of the corresponding SAM output. 503s 503s Output: 503s -t/--time print wall-clock time taken by search phases 503s --un write unpaired reads that didn't align to 503s --al write unpaired reads that aligned at least once to 503s --un-conc write pairs that didn't align concordantly to 503s --al-conc write pairs that aligned concordantly at least once to 503s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 503s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 503s --quiet print nothing to stderr except serious errors 503s --met-file send metrics to file at (off) 503s --met-stderr send metrics to stderr (off) 503s --met report internal counters & metrics every secs (1) 503s --no-unal suppress SAM records for unaligned reads 503s --no-head suppress header lines, i.e. lines starting with @ 503s --no-sq suppress @SQ header lines 503s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 503s --rg add ("lab:value") to @RG line of SAM header. 503s Note: @RG line only printed when --rg-id is set. 503s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 503s --sam-no-qname-trunc 503s Suppress standard behavior of truncating readname at first whitespace 503s at the expense of generating non-standard SAM. 503s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 503s --soft-clipped-unmapped-tlen 503s Exclude soft-clipped bases when reporting TLEN 503s --sam-append-comment 503s Append FASTA/FASTQ comment to SAM record 503s 503s Performance: 503s -p/--threads number of alignment threads to launch (1) 503s --reorder force SAM output order to match order of input reads 503s --mm use memory-mapped I/O for index; many 'bowtie's can share 503s 503s Other: 503s --qc-filter filter out reads that are bad according to QSEQ filter 503s --seed seed for random number generator (0) 503s --non-deterministic 503s seed rand. gen. arbitrarily instead of using read attributes 503s --version print version information and quit 503s -h/--help print this usage message 503s Error: Encountered internal Bowtie 2 exception (#1) 503s Command: /usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 503s (ERR): bowtie2-align exited with value 1 503s Cline 7 (fw:1, sam:1) 503s References: 503s >0 503s AGCATCGATCAGTATCTGA 503s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 503s 503s @HD VN:1.5 SO:unsorted GO:query 503s @SQ SN:0 LN:19 503s @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 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 503s 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 503s Cline 8 (fw:1, sam:1) 503s References: 503s >0 503s AGCATCGATCAGTATCTGA 503s /usr/bin/bowtie2 --trim5 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 504s @HD VN:1.5 SO:unsorted GO:query 504s @SQ SN:0 LN:19 504s @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 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 504s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 504s Cline 9 (fw:1, sam:1) 504s References: 504s >0 504s AGCATCGATCAGTATCTGA 504s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 504s @HD VN:1.5 SO:unsorted GO:query 504s @SQ SN:0 LN:19 504s @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 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 504s Cline multiread 1 (fw:1, sam:1) 504s References: 504s >0 504s AGCATCGATCAGTATCTGA 504s /usr/bin/bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 504s 504s 504s @HD VN:1.5 SO:unsorted GO:query 504s @SQ SN:0 LN:19 504s @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 -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 504s 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 504s 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 504s Cline multiread 2 (fw:1, sam:1) 504s References: 504s >0 504s AGCATCGATCAGTATCTGA 504s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 504s 504s 504s @HD VN:1.5 SO:unsorted GO:query 504s @SQ SN:0 LN:19 504s @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 -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 504s 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 504s Cline multiread 3 (fw:1, sam:1) 504s References: 504s >0 504s AGCATCGATCAGTATCTGA 504s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG 504s 504s @HD VN:1.5 SO:unsorted GO:query 504s @SQ SN:0 LN:19 504s @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 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" 504s 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 504s 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 504s Cline paired 1 (fw:1, sam:1) 504s References: 504s >0 504s AGCATCGATCAAAAACTGA 504s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 505s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII 505s @HD VN:1.5 SO:unsorted GO:query 505s @SQ SN:0 LN:19 505s @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" 505s 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 505s 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 505s 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 505s 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 505s Cline paired 2 (fw:1, sam:1) 505s References: 505s >0 505s AGCATCGATCAAAAACTGA 505s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 506s @HD VN:1.5 SO:unsorted GO:query 506s @SQ SN:0 LN:19 506s @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 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 506s 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 506s 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 506s Cline paired 3 (fw:1, sam:1) 506s References: 506s >0 506s AGCATCGATCAAAAACTGA 506s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 506s @HD VN:1.5 SO:unsorted GO:query 506s @SQ SN:0 LN:19 506s @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 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 506s 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 506s 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 506s Cline paired 4 (fw:1, sam:1) 506s References: 506s >0 506s AGCATCGATCAAAAACTGA 506s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII 506s @HD VN:1.5 SO:unsorted GO:query 506s @SQ SN:0 LN:19 506s @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 16 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" 506s 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 506s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 506s Fastq 1 (fw:1, sam:1) 506s References: 506s >0 506s AGCATCGATCAGTATCTGA 506s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 507s /usr/bin/bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz 507s @HD VN:1.5 SO:unsorted GO:query 507s @SQ SN:0 LN:19 507s @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.fq.gz" 507s 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 507s Fastq 2 (fw:1, sam:1) 507s References: 507s >0 507s AGCATCGATCAGTATCTGA 507s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz 507s @HD VN:1.5 SO:unsorted GO:query 507s @SQ SN:0 LN:19 507s @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 .simple_tests.fq.gz" 507s 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 507s Fastq 3 (fw:1, sam:1) 507s References: 507s >0 507s AGCATCGATCAGTATCTGA 507s /usr/bin/bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz 507s @HD VN:1.5 SO:unsorted GO:query 507s @SQ SN:0 LN:19 507s @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" 507s 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 507s Fastq 4 (fw:1, sam:1) 507s References: 507s >0 507s AGCATCGATCAGTATCTGA 507s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz 508s Error: Read r0 has more read characters than quality values. 508s terminate called after throwing an instance of 'int' 508s Aborted (core dumped) 508s (ERR): bowtie2-align exited with value 134 508s Fastq 5 (fw:1, sam:1) 508s References: 508s >0 508s AGCATCGATCAGTATCTGA 508s /usr/bin/bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz 508s Error: Read r0 has more read characters than quality values. 508s terminate called after throwing an instance of 'int' 509s Aborted (core dumped) 509s (ERR): bowtie2-align exited with value 134 509s Fastq 6 (fw:1, sam:1) 509s References: 509s >0 509s AGCATCGATCAGTATCTGA 509s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz 509s Error: reads file does not look like a FASTQ file 509s terminate called after throwing an instance of 'int' 510s Aborted (core dumped) 510s (ERR): bowtie2-align exited with value 134 510s Fastq 7 (fw:1, sam:1) 510s References: 510s >0 510s AGCATCGATCAGTATCTGA 510s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.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 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" 510s 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 510s Fastq 8 (fw:1, sam:1) 510s References: 510s >0 510s AGCATCGATCAGTATCTGA 510s /usr/bin/bowtie2 --trim5 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.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 --trim5 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" 510s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 510s Fastq 9 (fw:1, sam:1) 510s References: 510s >0 510s AGCATCGATCAGTATCTGA 510s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.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 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz" 510s Fastq multiread 1 (fw:1, sam:1) 510s References: 510s >0 510s AGCATCGATCAGTATCTGA 510s /usr/bin/bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.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 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz" 510s 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 510s 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 511s Fastq multiread 2 (fw:1, sam:1) 511s References: 511s >0 511s AGCATCGATCAGTATCTGA 511s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.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 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" 511s 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 511s Fastq multiread 3 (fw:1, sam:1) 511s References: 511s >0 511s AGCATCGATCAGTATCTGA 511s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.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 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz" 511s 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 511s 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 511s Fastq paired 1 (fw:1, sam:1) 511s References: 511s >0 511s AGCATCGATCAAAAACTGA 511s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 512s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 512s 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 512s 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 512s 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 512s 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 512s Fastq paired 2 (fw:1, sam:1) 512s References: 512s >0 512s AGCATCGATCAAAAACTGA 512s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 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 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 512s 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 512s 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 512s Fastq paired 3 (fw:1, sam:1) 512s References: 512s >0 512s AGCATCGATCAAAAACTGA 512s /usr/bin/bowtie2 -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 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 -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" 512s 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 512s 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 512s Fastq paired 4 (fw:1, sam:1) 512s References: 512s >0 512s AGCATCGATCAAAAACTGA 512s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 513s @HD VN:1.5 SO:unsorted GO:query 513s @SQ SN:0 LN:19 513s @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 7 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 513s 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 513s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 513s Fasta 1 (fw:1, sam:1) 513s References: 513s >0 513s AGCATCGATCAGTATCTGA 513s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 513s /usr/bin/bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz 514s @HD VN:1.5 SO:unsorted GO:query 514s @SQ SN:0 LN:19 514s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz" 514s 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 514s Fasta 2 (fw:1, sam:1) 514s References: 514s >0 514s AGCATCGATCAGTATCTGA 514s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz 514s @HD VN:1.5 SO:unsorted GO:query 514s @SQ SN:0 LN:19 514s @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 -f .simple_tests.fa.gz" 514s 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 514s Fasta 3 (fw:1, sam:1) 514s References: 514s >0 514s AGCATCGATCAGTATCTGA 514s /usr/bin/bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz 514s @HD VN:1.5 SO:unsorted GO:query 514s @SQ SN:0 LN:19 514s @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" 514s 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 514s Fasta 5 (fw:1, sam:1) 514s References: 514s >0 514s AGCATCGATCAGTATCTGA 514s /usr/bin/bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz 514s Error: reads file does not look like a FASTA file 514s terminate called after throwing an instance of 'int' 515s Aborted (core dumped) 515s (ERR): bowtie2-align exited with value 134 515s Fasta 6 (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz 515s Error: reads file does not look like a FASTA file 515s terminate called after throwing an instance of 'int' 515s Aborted (core dumped) 515s (ERR): bowtie2-align exited with value 134 515s Fasta 7 (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz 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 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" 516s 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 516s Fasta 8 (fw:1, sam:1) 516s References: 516s >0 516s AGCATCGATCAGTATCTGA 516s /usr/bin/bowtie2 --trim3 16 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz 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 --trim3 16 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz" 516s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 516s Fasta 9 (fw:1, sam:1) 516s References: 516s >0 516s AGCATCGATCAGTATCTGA 516s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz 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 -f .simple_tests.fa.gz" 516s Fasta multiread 1 (fw:1, sam:1) 516s References: 516s >0 516s AGCATCGATCAGTATCTGA 516s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz 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 11 -x .simple_tests.tmp -f .simple_tests.fa.gz" 516s 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 516s 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 516s Fasta multiread 2 (fw:1, sam:1) 516s References: 516s >0 516s AGCATCGATCAGTATCTGA 516s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.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 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.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 Fasta multiread 3 (fw:1, sam:1) 517s References: 517s >0 517s AGCATCGATCAGTATCTGA 517s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.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 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.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 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 517s Fasta multiline 1 (fw:1, sam:1) 517s References: 517s >0 517s AGCATCGATCAGTATCTGA 517s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.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 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.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 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 517s Fasta multiline 2 (fw:1, sam:1) 517s References: 517s >0 517s AGCATCGATCAGTATCTGA 517s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.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 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.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 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 517s Fasta multiline 3 (fw:1, sam:1) 517s References: 517s >0 517s AGCATCGATCAGTATCTGA 517s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.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 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz" 518s 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 518s 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 518s Fasta paired 1 (fw:1, sam:1) 518s References: 518s >0 518s AGCATCGATCAAAAACTGA 518s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 518s /usr/bin/bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.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 9 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.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 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 519s Fasta paired 2 (fw:1, sam:1) 519s References: 519s >0 519s AGCATCGATCAAAAACTGA 519s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.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 9 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.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 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 519s Fasta paired 3 (fw:1, sam:1) 519s References: 519s >0 519s AGCATCGATCAAAAACTGA 519s /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 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 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.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 Fasta paired 4 (fw:1, sam:1) 519s References: 519s >0 519s AGCATCGATCAAAAACTGA 519s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.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 -3 7 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 519s 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 519s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 519s Raw 1 (fw:1, sam:1) 519s References: 519s >0 519s AGCATCGATCAGTATCTGA 519s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 520s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.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 2 -x .simple_tests.tmp -r .simple_tests.raw.gz" 520s 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 520s Raw 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 -r .simple_tests.raw.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 1 -x .simple_tests.tmp -r .simple_tests.raw.gz" 521s 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 521s Raw 3 (fw:1, sam:1) 521s References: 521s >0 521s AGCATCGATCAGTATCTGA 521s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.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 11 -x .simple_tests.tmp -r .simple_tests.raw.gz" 521s 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 521s Raw 7 (fw:1, sam:1) 521s References: 521s >0 521s AGCATCGATCAGTATCTGA 521s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.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 1 -x .simple_tests.tmp -r .simple_tests.raw.gz" 521s 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 521s Raw 8 (fw:1, sam:1) 521s References: 521s >0 521s AGCATCGATCAGTATCTGA 521s /usr/bin/bowtie2 --trim3 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.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 3 -x .simple_tests.tmp -r .simple_tests.raw.gz" 521s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 521s Raw 9 (fw:1, sam:1) 521s References: 521s >0 521s AGCATCGATCAGTATCTGA 521s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.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 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz" 522s Raw multiread 1 (fw:1, sam:1) 522s References: 522s >0 522s AGCATCGATCAGTATCTGA 522s /usr/bin/bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.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 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz" 522s 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 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 Raw multiread 2 (fw:1, sam:1) 522s References: 522s >0 522s AGCATCGATCAGTATCTGA 522s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.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 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" 522s 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 522s Raw multiread 3 (fw:1, sam:1) 522s References: 522s >0 522s AGCATCGATCAGTATCTGA 522s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.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 10 -x .simple_tests.tmp -r .simple_tests.raw.gz" 522s 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 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 Raw 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 -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.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 8 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 523s 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 523s 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 523s 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 523s 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 523s Raw paired 2 (fw:1, sam:1) 523s References: 523s >0 523s AGCATCGATCAAAAACTGA 523s /usr/bin/bowtie2 -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 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 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 524s 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 524s 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 524s Raw paired 3 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAAAAACTGA 524s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.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 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 524s 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 524s 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 524s Raw paired 4 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAAAAACTGA 524s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.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 -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 524s 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 524s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 524s Tabbed 1 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAGTATCTGA 524s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 525s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -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 10 -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 6 -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 6 -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 3 (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 @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 12 -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' 527s Aborted (core dumped) 527s (ERR): bowtie2-align exited with value 134 527s Tabbed 5 (fw:1, sam:1) 527s References: 527s >0 527s AGCATCGATCAGTATCTGA 527s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 527s Error: Read r0 has more quality values than read characters. 527s terminate called after throwing an instance of 'int' 528s Aborted (core dumped) 528s (ERR): bowtie2-align exited with value 134 528s Tabbed 7 (fw:1, sam:1) 528s References: 528s >0 528s AGCATCGATCAGTATCTGA 528s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 11 -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 --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 528s 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 528s Tabbed 8 (fw:1, sam:1) 528s References: 528s >0 528s AGCATCGATCAGTATCTGA 528s /usr/bin/bowtie2 --trim5 16 --quiet -a --reads-per-batch 1 -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 --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 528s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 528s Tabbed 9 (fw:1, sam:1) 528s References: 528s >0 528s AGCATCGATCAGTATCTGA 528s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 15 -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 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 528s Tabbed multiread 1 (fw:1, sam:1) 528s References: 528s >0 528s AGCATCGATCAGTATCTGA 528s /usr/bin/bowtie2 --quiet -a --reads-per-batch 8 -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 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 528s 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 528s 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 528s Tabbed multiread 2 (fw:1, sam:1) 528s References: 528s >0 528s AGCATCGATCAGTATCTGA 529s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.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 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 529s 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 529s Tabbed multiread 3 (fw:1, sam:1) 529s References: 529s >0 529s AGCATCGATCAGTATCTGA 529s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.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 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 529s 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 529s 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 529s Tabbed paired 1 (fw:1, sam:1) 529s References: 529s >0 529s AGCATCGATCAAAAACTGA 529s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 530s /usr/bin/bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.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 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 530s 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 530s 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 530s 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 530s 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 530s Tabbed paired 2 (fw:1, sam:1) 530s References: 530s >0 530s AGCATCGATCAAAAACTGA 530s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.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 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 530s 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 530s 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 530s Tabbed paired 3 (fw:1, sam:1) 530s References: 530s >0 530s AGCATCGATCAAAAACTGA 530s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.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 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 530s 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 530s 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 530s Tabbed paired 4 (fw:1, sam:1) 530s References: 530s >0 530s AGCATCGATCAAAAACTGA 530s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 531s @HD VN:1.5 SO:unsorted GO:query 531s @SQ SN:0 LN:19 531s @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 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 531s 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 531s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 531s Qseq 1 (fw:1, sam:1) 531s References: 531s >0 531s AGCATCGATCAGTATCTGA 531s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 531s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 532s @HD VN:1.5 SO:unsorted GO:query 532s @SQ SN:0 LN:19 532s @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 --qseq .simple_tests_qseq.txt.gz" 532s 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 532s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 532s Qseq 2 (fw:1, sam:1) 532s References: 532s >0 532s AGCATCGATCAGTATCTGA 532s /usr/bin/bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 532s @HD VN:1.5 SO:unsorted GO:query 532s @SQ SN:0 LN:19 532s @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 --qseq .simple_tests_qseq.txt.gz" 532s 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 532s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 532s Qseq 3 (fw:1, sam:1) 532s References: 532s >0 532s AGCATCGATCAGTATCTGA 532s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 532s @HD VN:1.5 SO:unsorted GO:query 532s @SQ SN:0 LN:19 532s @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 --qseq .simple_tests_qseq.txt.gz" 532s 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 532s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 532s Qseq 4 (fw:1, sam:1) 532s References: 532s >0 532s AGCATCGATCAGTATCTGA 532s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 532s Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values. 532s terminate called after throwing an instance of 'int' 533s Aborted (core dumped) 533s (ERR): bowtie2-align exited with value 134 533s Qseq 7 (fw:1, sam:1) 533s References: 533s >0 533s AGCATCGATCAGTATCTGA 533s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 533s @HD VN:1.5 SO:unsorted GO:query 533s @SQ SN:0 LN:19 533s @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" 533s 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 533s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 533s Qseq 8 (fw:1, sam:1) 533s References: 533s >0 533s AGCATCGATCAGTATCTGA 533s /usr/bin/bowtie2 --trim3 16 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 533s @HD VN:1.5 SO:unsorted GO:query 533s @SQ SN:0 LN:19 533s @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 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 533s MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 533s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 533s Qseq 9 (fw:1, sam:1) 533s References: 533s >0 533s AGCATCGATCAGTATCTGA 533s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 533s @HD VN:1.5 SO:unsorted GO:query 533s @SQ SN:0 LN:19 533s @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" 533s Qseq multiread 1 (fw:1, sam:1) 533s References: 533s >0 533s AGCATCGATCAGTATCTGA 533s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 534s @HD VN:1.5 SO:unsorted GO:query 534s @SQ SN:0 LN:19 534s @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" 534s 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 534s 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 534s Qseq multiread 2 (fw:1, sam:1) 534s References: 534s >0 534s AGCATCGATCAGTATCTGA 534s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 534s @HD VN:1.5 SO:unsorted GO:query 534s @SQ SN:0 LN:19 534s @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 --qseq .simple_tests_qseq.txt.gz" 534s 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 534s Qseq multiread 3 (fw:1, sam:1) 534s References: 534s >0 534s AGCATCGATCAGTATCTGA 534s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 534s @HD VN:1.5 SO:unsorted GO:query 534s @SQ SN:0 LN:19 534s @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 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 534s 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 534s 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 534s Qseq paired 1 (fw:1, sam:1) 534s References: 534s >0 534s AGCATCGATCAAAAACTGA 534s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 535s /usr/bin/bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz 535s @HD VN:1.5 SO:unsorted GO:query 535s @SQ SN:0 LN:19 535s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 535s 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 535s 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 535s 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 535s 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 535s Qseq paired 2 (fw:1, sam:1) 535s References: 535s >0 535s AGCATCGATCAAAAACTGA 535s /usr/bin/bowtie2 -s 1 --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 535s @HD VN:1.5 SO:unsorted GO:query 535s @SQ SN:0 LN:19 535s @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 5 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 535s 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 535s 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 535s Left-align insertion (fw:1, sam:1) 535s References: 535s >0 535s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 535s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 536s /usr/bin/bowtie2 --quiet --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 536s @HD VN:1.5 SO:unsorted GO:query 536s @SQ SN:0 LN:73 536s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 536s 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 536s Left-align deletion (fw:1, sam:1) 536s References: 536s >0 536s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 536s /usr/bin/bowtie2 --quiet --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 537s @HD VN:1.5 SO:unsorted GO:query 537s @SQ SN:0 LN:73 537s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 537s 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 537s Left-align insertion with mismatch at LHS (fw:1, sam:1) 537s References: 537s >0 537s GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 537s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 537s /usr/bin/bowtie2 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:73 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 538s 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 538s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 538s References: 538s >0 538s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 538s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 538s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:1192 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --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" 538s 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 538s 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 538s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 538s References: 538s >0 538s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG 538s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 539s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 539s @HD VN:1.5 SO:unsorted GO:query 539s @SQ SN:0 LN:1028 539s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 539s 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 539s 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 539s MREVERSE flag is set if mate does not align (fw:1, sam:1) 539s References: 539s >0 539s TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG 539s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 540s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 540s @HD VN:1.5 SO:unsorted GO:query 540s @SQ SN:0 LN:250 540s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 540s 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 540s r0 165 0 51 0 * = 51 0 CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 540s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 540s References: 540s >0 540s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 540s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 541s /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 541s @HD VN:1.5 SO:unsorted GO:query 541s @SQ SN:0 LN:290 541s @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" 541s 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 541s 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 541s MD:Z 1 (fw:1, sam:1) 541s References: 541s >0 541s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 541s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 542s /usr/bin/bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 542s @HD VN:1.5 SO:unsorted GO:query 542s @SQ SN:0 LN:54 542s @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" 542s 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 542s MD:Z 1 (fw:0, sam:1) 542s References: 542s >0 542s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 542s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:54 543s @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" 543s 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 543s MD:Z 2 (fw:1, sam:1) 543s References: 543s >0 543s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 543s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 543s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 544s @HD VN:1.5 SO:unsorted GO:query 544s @SQ SN:0 LN:54 544s @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 .simple_tests.1a.fq.gz" 544s 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 544s MD:Z 2 (fw:0, sam:1) 544s References: 544s >0 544s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 544s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 544s @HD VN:1.5 SO:unsorted GO:query 544s @SQ SN:0 LN:54 544s @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" 544s 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 544s MD:Z 3 (fw:1, sam:1) 544s References: 544s >0 544s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 544s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 545s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 545s @HD VN:1.5 SO:unsorted GO:query 545s @SQ SN:0 LN:55 545s @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" 545s 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 545s MD:Z 3 (fw:0, sam:1) 545s References: 545s >0 545s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 545s /usr/bin/bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 545s @HD VN:1.5 SO:unsorted GO:query 545s @SQ SN:0 LN:55 545s @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 -q .simple_tests.1a.fq.gz" 545s 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 545s MD:Z 4 (fw:1, sam:1) 545s References: 545s >0 545s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 545s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 546s /usr/bin/bowtie2 --quiet -a --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:55 546s @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" 546s 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 546s MD:Z 4 (fw:0, sam:1) 546s References: 546s >0 546s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 546s /usr/bin/bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 546s @HD VN:1.5 SO:unsorted GO:query 546s @SQ SN:0 LN:55 546s @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" 546s 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 546s Local alignment 1 (fw:1, sam:1) 546s References: 546s >0 546s TTGT 546s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 547s /usr/bin/bowtie2 --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 547s @HD VN:1.5 SO:unsorted GO:query 547s @SQ SN:0 LN:4 547s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 547s 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 547s Local alignment 1 (fw:0, sam:1) 547s References: 547s >0 547s TTGT 547s /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 548s @HD VN:1.5 SO:unsorted GO:query 548s @SQ SN:0 LN:4 548s @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" 548s 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 548s Local alignment 2 (fw:1, sam:1) 548s References: 548s >0 548s TTGA 548s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 548s /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 549s @HD VN:1.5 SO:unsorted GO:query 549s @SQ SN:0 LN:4 549s @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" 549s 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 549s Local alignment 2 (fw:0, sam:1) 549s References: 549s >0 549s TTGA 549s /usr/bin/bowtie2 --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --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:4 549s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 549s 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 549s Local alignment 3 (fw:1, sam:1) 549s References: 549s >0 549s TTGTTCGTTTGTTCGT 549s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 550s /usr/bin/bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:16 550s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 550s 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 550s 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 550s Local alignment 3 (fw:0, sam:1) 550s References: 550s >0 550s TTGTTCGTTTGTTCGT 550s /usr/bin/bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:16 550s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 550s 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 550s 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 550s Local alignment 4 (fw:1, sam:1) 550s References: 550s >0 550s TTGTTCGTTTGTTCGT 550s /usr/bin/bowtie2 --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:16 550s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 550s 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 550s 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 550s Local alignment 4 (fw:0, sam:1) 550s References: 550s >0 550s TTGTTCGTTTGTTCGT 550s /usr/bin/bowtie2 --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 551s @HD VN:1.5 SO:unsorted GO:query 551s @SQ SN:0 LN:16 551s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 551s 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 551s 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 551s Alignment order -k (fw:1, sam:1) 551s References: 551s >0 551s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 551s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 552s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 552s @HD VN:1.5 SO:unsorted GO:query 552s @SQ SN:0 LN:86 552s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 552s 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 552s 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 552s 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 552s 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 552s Alignment order -k (fw:0, sam:1) 552s References: 552s >0 552s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 552s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 552s @HD VN:1.5 SO:unsorted GO:query 552s @SQ SN:0 LN:86 552s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 552s 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 552s 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 552s 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 552s 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 552s Alignment order -a (fw:1, sam:1) 552s References: 552s >0 552s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 552s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 552s @HD VN:1.5 SO:unsorted GO:query 552s @SQ SN:0 LN:86 552s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 552s 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 552s 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 552s 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 552s 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 552s Alignment order -a (fw:0, sam:1) 552s References: 552s >0 552s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 552s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 553s @HD VN:1.5 SO:unsorted GO:query 553s @SQ SN:0 LN:86 553s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 553s 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 553s 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 553s 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 553s 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 553s Mate reporting order, -a (fw:1, sam:1) 553s References: 553s >0 553s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 553s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 553s /usr/bin/bowtie2 --fr --quiet -a --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 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:407 554s @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,.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" 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s Mate reporting order, -a (fw:0, sam:1) 554s References: 554s >0 554s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 554s /usr/bin/bowtie2 --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 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:407 554s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --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" 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s Mate reporting order, -M 1 (fw:1, sam:1) 554s References: 554s >0 554s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 554s /usr/bin/bowtie2 --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 554s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:407 554s @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 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" 554s 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 554s 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 554s 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 554s 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 554s 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 554s 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 554s Mate reporting order, -M 1 (fw:0, sam:1) 554s References: 554s >0 554s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 554s /usr/bin/bowtie2 --fr --quiet -M 1 --reads-per-batch 7 -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 555s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 555s @HD VN:1.5 SO:unsorted GO:query 555s @SQ SN:0 LN:407 555s @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 7 -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" 555s 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 555s 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 555s 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 555s 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 555s 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 555s 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 555s Non-overlapping; no args (fw:1, sam:1) 555s References: 555s >0 555s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 555s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 555s /usr/bin/bowtie2 --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 556s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 556s @HD VN:1.5 SO:unsorted GO:query 556s @SQ SN:0 LN:47 556s @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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 556s 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 556s 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 556s Non-overlapping; no args (fw:0, sam:1) 556s References: 556s >0 556s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 556s /usr/bin/bowtie2 --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 556s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 556s @HD VN:1.5 SO:unsorted GO:query 556s @SQ SN:0 LN:47 556s @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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 556s 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 556s 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 556s Non-overlapping; --no-discordant (fw:1, sam:1) 556s References: 556s >0 556s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 556s /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 556s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 556s @HD VN:1.5 SO:unsorted GO:query 556s @SQ SN:0 LN:47 556s @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" 556s 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 556s 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 556s Non-overlapping; --no-discordant (fw:0, sam:1) 556s References: 556s >0 556s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 556s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 556s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:47 557s @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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 557s 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 557s 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 557s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 557s References: 557s >0 557s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 557s /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 557s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:47 557s @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" 557s 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 557s 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 557s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 557s References: 557s >0 557s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 557s /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 557s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:47 557s @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" 557s 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 557s 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 557s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 557s References: 557s >0 557s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 557s /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 557s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:47 557s @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" 557s 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 557s 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 557s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 557s References: 557s >0 557s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 557s /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 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:47 558s @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" 558s 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 558s 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 558s Non-overlapping; --no-dovetail (fw:1, sam:1) 558s References: 558s >0 558s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 558s /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 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:47 558s @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" 558s 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 558s 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 558s Non-overlapping; --no-dovetail (fw:0, sam:1) 558s References: 558s >0 558s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 558s /usr/bin/bowtie2 --no-dovetail --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 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:47 558s @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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 558s 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 558s 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 558s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1) 558s References: 558s >0 558s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 558s /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 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:47 558s @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" 558s 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 558s 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 558s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1) 558s References: 558s >0 558s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 558s /usr/bin/bowtie2 --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 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:47 559s @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 4 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 559s 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 559s 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 559s Non-overlapping; --no-overlap (fw:1, sam:1) 559s References: 559s >0 559s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 559s /usr/bin/bowtie2 --no-overlap --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 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:47 559s @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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 559s 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 559s 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 559s Non-overlapping; --no-overlap (fw:0, sam:1) 559s References: 559s >0 559s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 559s /usr/bin/bowtie2 --no-overlap --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 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:47 559s @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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 559s 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 559s 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 559s Overlapping; no args (fw:1, sam:1) 559s References: 559s >0 559s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 559s /usr/bin/bowtie2 --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 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:47 560s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 560s 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 560s 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 560s Overlapping; no args (fw:0, sam:1) 560s References: 560s >0 560s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 560s /usr/bin/bowtie2 --ff --quiet -M 1 --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:47 560s @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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 560s 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 560s 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 560s Overlapping; --no-dovetail (fw:1, sam:1) 560s References: 560s >0 560s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 560s /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 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:47 560s @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" 560s 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 560s 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 560s Overlapping; --no-dovetail (fw:0, sam:1) 560s References: 560s >0 560s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 560s /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 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:47 560s @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" 560s 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 560s 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 560s Overlapping; --no-contain (fw:1, sam:1) 560s References: 560s >0 560s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 560s /usr/bin/bowtie2 --no-contain --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 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:47 561s @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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s 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 561s 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 561s Overlapping; --no-contain (fw:0, sam:1) 561s References: 561s >0 561s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 561s /usr/bin/bowtie2 --no-contain --ff --quiet -M 1 --reads-per-batch 15 -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:47 561s @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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s 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 561s 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 561s Overlapping; --no-overlap (fw:1, sam:1) 561s References: 561s >0 561s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 561s /usr/bin/bowtie2 --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 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:47 561s @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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s 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 561s 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 561s Overlapping; --no-overlap (fw:0, sam:1) 561s References: 561s >0 561s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 561s /usr/bin/bowtie2 --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 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:47 561s @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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s 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 561s 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 562s Scoring params 1 (fw:1, sam:1) 562s References: 562s >0 562s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 562s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 562s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.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:105 563s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 563s 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 563s Scoring params 1 (fw:0, sam:1) 563s References: 563s >0 563s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 563s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.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:105 563s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 563s 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 563s Scoring params 2 (fw:1, sam:1) 563s References: 563s >0 563s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 563s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 564s /usr/bin/bowtie2 --ignore-quals --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 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:102 564s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 564s 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 564s Scoring params 2 (fw:0, sam:1) 564s References: 564s >0 564s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 564s /usr/bin/bowtie2 --ignore-quals --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 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:102 564s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 564s 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 564s Scoring params 3 (fw:1, sam:1) 564s References: 564s >0 564s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 564s /usr/bin/bowtie2 --ignore-quals --rfg 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 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:102 564s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 564s 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 564s Scoring params 3 (fw:0, sam:1) 564s References: 564s >0 564s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 564s /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 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:102 565s @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" 565s 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 565s Scoring params 4 (fw:1, sam:1) 565s References: 565s >0 565s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 565s /usr/bin/bowtie2 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -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:102 565s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s 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 565s Scoring params 4 (fw:0, sam:1) 565s References: 565s >0 565s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 565s /usr/bin/bowtie2 --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 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:102 565s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s 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 565s Scoring params 5 (fw:1, sam:1) 565s References: 565s >0 565s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 565s /usr/bin/bowtie2 --ignore-quals --mp 8 --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 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:102 565s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s 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 565s Scoring params 5 (fw:0, sam:1) 565s References: 565s >0 565s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 565s /usr/bin/bowtie2 --ignore-quals --mp 8 --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 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:102 566s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s 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 566s Scoring params 6 (fw:1, sam:1) 566s References: 566s >0 566s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 566s /usr/bin/bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -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:102 566s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s 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 566s Scoring params 6 (fw:0, sam:1) 566s References: 566s >0 566s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 566s /usr/bin/bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -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:102 566s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s 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 566s Q XS:i 1a (fw:1, sam:1) 566s References: 566s >0 566s TTGTTCGATTGTTCGA 566s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 567s /usr/bin/bowtie2 --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 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:16 567s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 567s 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 567s Q XS:i 1a (fw:0, sam:1) 567s References: 567s >0 567s TTGTTCGATTGTTCGA 567s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -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:16 568s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s 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 568s Q XS:i 1a ! --mp 3,3 (fw:1, sam:1) 568s References: 568s >0 568s TTGTTCGATTGTTCGA 568s /usr/bin/bowtie2 -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 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:16 568s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s 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 568s Q XS:i 1a ! --mp 3,3 (fw:0, sam:1) 568s References: 568s >0 568s TTGTTCGATTGTTCGA 568s /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 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:16 568s @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" 568s 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 568s Q XS:i 1a ! --mp 3,6 (fw:1, sam:1) 568s References: 568s >0 568s TTGTTCGATTGTTCGA 568s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -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:16 568s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s 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 568s Q XS:i 1a ! --mp 3,6 (fw:0, sam:1) 568s References: 568s >0 568s TTGTTCGATTGTTCGA 568s /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 569s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 569s 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 569s Q XS:i 1a I --mp 3,3 (fw:1, sam:1) 569s References: 569s >0 569s TTGTTCGATTGTTCGA 569s /usr/bin/bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 569s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 569s 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 569s Q XS:i 1a I --mp 3,3 (fw:0, sam:1) 569s References: 569s >0 569s TTGTTCGATTGTTCGA 569s /usr/bin/bowtie2 -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 569s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 569s 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 569s Q XS:i 1a I --mp 3,6 (fw:1, sam:1) 569s References: 569s >0 569s TTGTTCGATTGTTCGA 569s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 569s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 569s 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 569s Q XS:i 1a I --mp 3,6 (fw:0, sam:1) 569s References: 569s >0 569s TTGTTCGATTGTTCGA 569s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 570s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 570s @HD VN:1.5 SO:unsorted GO:query 570s @SQ SN:0 LN:16 570s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 570s 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 570s Q XS:i 1a --ignore-quals (fw:1, sam:1) 570s References: 570s >0 570s TTGTTCGATTGTTCGA 570s /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 570s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 570s @HD VN:1.5 SO:unsorted GO:query 570s @SQ SN:0 LN:16 570s @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" 570s 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 570s Q XS:i 1a --ignore-quals (fw:0, sam:1) 570s References: 570s >0 570s TTGTTCGATTGTTCGA 570s /usr/bin/bowtie2 --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 570s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 570s @HD VN:1.5 SO:unsorted GO:query 570s @SQ SN:0 LN:16 570s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 570s 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 570s Q XS:i 1b (fw:1, sam:1) 570s References: 570s >0 570s TTGTTCGATTGTTCGA 570s /usr/bin/bowtie2 --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 570s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 570s @HD VN:1.5 SO:unsorted GO:query 570s @SQ SN:0 LN:16 570s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 570s 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 570s Q XS:i 1b (fw:0, sam:1) 570s References: 570s >0 570s TTGTTCGATTGTTCGA 570s /usr/bin/bowtie2 --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 571s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --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" 571s 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 571s Q XS:i 1b --ignore-quals (fw:1, sam:1) 571s References: 571s >0 571s TTGTTCGATTGTTCGA 571s /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 571s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --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" 571s 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 571s Q XS:i 1b --ignore-quals (fw:0, sam:1) 571s References: 571s >0 571s TTGTTCGATTGTTCGA 571s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s 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 571s Q XS:i 1c (fw:1, sam:1) 571s References: 571s >0 571s TTGTTCGATTGTTCGA 571s /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 571s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --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" 571s 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 571s Q XS:i 1c (fw:0, sam:1) 571s References: 571s >0 571s TTGTTCGATTGTTCGA 571s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 572s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 572s 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 572s Q XS:i 1c --ignore-quals (fw:1, sam:1) 572s References: 572s >0 572s TTGTTCGATTGTTCGA 572s /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 572s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --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" 572s 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 572s Q XS:i 1c --ignore-quals (fw:0, sam:1) 572s References: 572s >0 572s TTGTTCGATTGTTCGA 572s /usr/bin/bowtie2 --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 572s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 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 --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" 572s 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 572s (fw:1, sam:1) 572s References: 572s >0 572s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 572s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 573s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 573s @HD VN:1.5 SO:unsorted GO:query 573s @SQ SN:0 LN:68 573s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 573s 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 573s r0 133 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 573s (fw:0, sam:1) 573s References: 573s >0 573s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 573s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 573s @HD VN:1.5 SO:unsorted GO:query 573s @SQ SN:0 LN:68 573s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --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" 573s 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 573s r0 69 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 573s (fw:1, sam:1) 573s References: 573s >0 573s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 573s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 574s /usr/bin/bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 574s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 574s @HD VN:1.5 SO:unsorted GO:query 574s @SQ SN:0 LN:528 574s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 574s 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 574s (fw:0, sam:1) 574s References: 574s >0 574s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 574s /usr/bin/bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 574s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 574s @HD VN:1.5 SO:unsorted GO:query 574s @SQ SN:0 LN:528 574s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 574s 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 574s (fw:1, sam:1) 574s References: 574s >0 574s TTGTTCGTTTGTTCGT 574s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 575s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 575s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 575s @HD VN:1.5 SO:unsorted GO:query 575s @SQ SN:0 LN:16 575s @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" 575s 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 575s (fw:0, sam:1) 575s References: 575s >0 575s TTGTTCGTTTGTTCGT 575s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 576s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 576s @HD VN:1.5 SO:unsorted GO:query 576s @SQ SN:0 LN:16 576s @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" 576s 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 576s (fw:1, sam:1) 576s References: 576s >0 576s TTGTTCGTTTGTTCGT 576s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 576s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 576s @HD VN:1.5 SO:unsorted GO:query 576s @SQ SN:0 LN:16 576s @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" 576s 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 576s (fw:0, sam:1) 576s References: 576s >0 576s TTGTTCGTTTGTTCGT 576s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 576s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 576s @HD VN:1.5 SO:unsorted GO:query 576s @SQ SN:0 LN:16 576s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 576s 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 576s XS:i 1 (fw:1, sam:1) 576s References: 576s >0 576s TTGTTCGATTGTTCGA 576s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 577s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 577s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 577s @HD VN:1.5 SO:unsorted GO:query 577s @SQ SN:0 LN:16 577s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 577s 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 577s XS:i 1 (fw:0, sam:1) 577s References: 577s >0 577s TTGTTCGATTGTTCGA 577s /usr/bin/bowtie2 --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 577s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 577s @HD VN:1.5 SO:unsorted GO:query 577s @SQ SN:0 LN:16 577s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 577s 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 577s XS:i 2 (fw:1, sam:1) 577s References: 577s >0 577s TTGTTCGATTGTTCGA 577s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 577s @HD VN:1.5 SO:unsorted GO:query 577s @SQ SN:0 LN:16 577s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 577s r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU 577s XS:i 2 (fw:0, sam:1) 577s References: 577s >0 577s TTGTTCGATTGTTCGA 577s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --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:16 578s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 578s r0 4 * 0 0 * * 0 0 ACGAACAA IIIIIIII YT:Z:UU 578s XS:i 3a (fw:1, sam:1) 578s References: 578s >0 578s TTGTTCGATTGTTCGT 578s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 578s /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 579s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:16 579s @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" 579s 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 579s XS:i 3a (fw:0, sam:1) 579s References: 579s >0 579s TTGTTCGATTGTTCGT 579s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 579s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:16 579s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 579s 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 579s XS:i 3b (fw:1, sam:1) 579s References: 579s >0 579s TTGTTCGATTGTTCGT 579s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 579s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:16 579s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 579s 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 579s XS:i 3b (fw:0, sam:1) 579s References: 579s >0 579s TTGTTCGATTGTTCGT 579s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 579s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:16 579s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 579s 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 579s XS:i 3c (fw:1, sam:1) 579s References: 579s >0 579s TTGTTCGATTGTTCGT 579s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 579s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:16 579s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 579s 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 580s XS:i 3c (fw:0, sam:1) 580s References: 580s >0 580s TTGTTCGATTGTTCGT 580s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 580s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 580s @HD VN:1.5 SO:unsorted GO:query 580s @SQ SN:0 LN:16 580s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 580s 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 580s XS:i 4a (fw:1, sam:1) 580s References: 580s >0 580s TTGTTCAATTGTTCGATTGTTCGT 580s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 581s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 581s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 581s @HD VN:1.5 SO:unsorted GO:query 581s @SQ SN:0 LN:24 581s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 581s 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 581s XS:i 4a (fw:0, sam:1) 581s References: 581s >0 581s TTGTTCAATTGTTCGATTGTTCGT 581s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 581s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 581s @HD VN:1.5 SO:unsorted GO:query 581s @SQ SN:0 LN:24 581s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 581s 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 581s XS:i 4b (fw:1, sam:1) 581s References: 581s >0 581s TTGTTCAATTGTTCGATTGTTCGT 581s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 581s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 581s @HD VN:1.5 SO:unsorted GO:query 581s @SQ SN:0 LN:24 581s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 581s 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 581s XS:i 4b (fw:0, sam:1) 581s References: 581s >0 581s TTGTTCAATTGTTCGATTGTTCGT 581s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 581s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 581s @HD VN:1.5 SO:unsorted GO:query 581s @SQ SN:0 LN:24 581s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 581s 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 581s XS:i 5a (fw:1, sam:1) 581s References: 581s >0 581s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 581s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 582s /usr/bin/bowtie2 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.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:120 582s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 582s 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 582s XS:i 5a (fw:0, sam:1) 582s References: 582s >0 582s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 582s /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 583s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 583s @HD VN:1.5 SO:unsorted GO:query 583s @SQ SN:0 LN:120 583s @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" 583s 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 583s XS:i 5b (fw:1, sam:1) 583s References: 583s >0 583s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 583s /usr/bin/bowtie2 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 583s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 583s @HD VN:1.5 SO:unsorted GO:query 583s @SQ SN:0 LN:120 583s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 583s 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 583s XS:i 5b (fw:0, sam:1) 583s References: 583s >0 583s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 583s /usr/bin/bowtie2 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 583s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 583s @HD VN:1.5 SO:unsorted GO:query 583s @SQ SN:0 LN:120 583s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 583s 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 583s BWA-SW-like 1 (fw:1, sam:1) 583s References: 583s >0 583s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 583s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 584s /usr/bin/bowtie2 --bwa-sw-like --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 584s @HD VN:1.5 SO:unsorted GO:query 584s @SQ SN:0 LN:64 584s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 584s 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 584s BWA-SW-like 1 (fw:0, sam:1) 584s References: 584s >0 584s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 584s /usr/bin/bowtie2 --bwa-sw-like --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 584s @HD VN:1.5 SO:unsorted GO:query 584s @SQ SN:0 LN:64 584s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 584s 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 584s BWA-SW-like 2 (fw:1, sam:1) 584s References: 584s >0 584s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 584s /usr/bin/bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 585s @HD VN:1.5 SO:unsorted GO:query 585s @SQ SN:0 LN:64 585s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 585s 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 585s BWA-SW-like 2 (fw:0, sam:1) 585s References: 585s >0 585s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 585s /usr/bin/bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 585s @HD VN:1.5 SO:unsorted GO:query 585s @SQ SN:0 LN:64 585s @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" 585s 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 585s BWA-SW-like 3 (fw:1, sam:1) 585s References: 585s >0 585s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 585s /usr/bin/bowtie2 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 585s @HD VN:1.5 SO:unsorted GO:query 585s @SQ SN:0 LN:64 585s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 585s 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 585s BWA-SW-like 3 (fw:0, sam:1) 585s References: 585s >0 585s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 585s /usr/bin/bowtie2 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 585s @HD VN:1.5 SO:unsorted GO:query 585s @SQ SN:0 LN:64 585s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 585s 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 585s SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1) 585s References: 585s >0 585s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 585s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 586s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 586s @HD VN:1.5 SO:unsorted GO:query 586s @SQ SN:0 LN:69 586s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 586s 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 586s 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 586s SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1) 586s References: 586s >0 586s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 586s /usr/bin/bowtie2 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 587s @HD VN:1.5 SO:unsorted GO:query 587s @SQ SN:0 LN:69 587s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 587s 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 587s 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 587s SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1) 587s References: 587s >0 587s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 587s /usr/bin/bowtie2 --rf --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 587s @HD VN:1.5 SO:unsorted GO:query 587s @SQ SN:0 LN:69 587s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 587s 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 587s 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 587s SAM paired-end where both mates align 1 (fw:1, sam:1) 587s References: 587s >0 587s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 587s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 587s @HD VN:1.5 SO:unsorted GO:query 587s @SQ SN:0 LN:69 587s @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 -2 .simple_tests.2a.fq.gz" 587s 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 587s 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 587s SAM paired-end where both mates align 2 (fw:1, sam:1) 587s References: 587s >0 587s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 587s /usr/bin/bowtie2 --rf --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 587s @HD VN:1.5 SO:unsorted GO:query 587s @SQ SN:0 LN:69 587s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 587s 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 587s 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 587s SAM paired-end where both mates align 3 (fw:1, sam:1) 587s References: 587s >0 587s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 587s /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 588s @HD VN:1.5 SO:unsorted GO:query 588s @SQ SN:0 LN:69 588s @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" 588s 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 588s 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 588s SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1) 588s References: 588s >0 588s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 588s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 588s @HD VN:1.5 SO:unsorted GO:query 588s @SQ SN:0 LN:69 588s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --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" 588s 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 588s r0 133 0 4 0 * = 4 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 588s SAM paired-end where neither mate aligns (fw:1, sam:1) 588s References: 588s >0 588s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 588s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 588s @HD VN:1.5 SO:unsorted GO:query 588s @SQ SN:0 LN:69 588s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 588s r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 588s r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 588s SAM paired-end where both mates align, but discordantly (fw:1, sam:1) 588s References: 588s >0 588s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 588s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 588s @HD VN:1.5 SO:unsorted GO:query 588s @SQ SN:0 LN:69 588s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --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" 588s 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 588s 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 588s matchesRef regression 4 (fw:1, sam:1) 588s References: 588s >0 588s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 588s >1 588s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 588s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 589s /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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 589s @HD VN:1.5 SO:unsorted GO:query 589s @SQ SN:0 LN:120 589s @SQ SN:1 LN:31 589s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 589s r0 4 * 0 0 * * 0 0 ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 589s matchesRef regression 4 (fw:0, sam:1) 589s References: 589s >0 589s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 589s >1 589s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 589s /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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 590s @HD VN:1.5 SO:unsorted GO:query 590s @SQ SN:0 LN:120 590s @SQ SN:1 LN:31 590s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 590s r0 4 * 0 0 * * 0 0 GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 590s matchesRef regression 3 (fw:1, sam:1) 590s References: 590s >0 590s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 590s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 590s /usr/bin/bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 591s @HD VN:1.5 SO:unsorted GO:query 591s @SQ SN:0 LN:53 591s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 591s 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 591s matchesRef regression 3 (fw:0, sam:1) 591s References: 591s >0 591s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 591s /usr/bin/bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 591s @HD VN:1.5 SO:unsorted GO:query 591s @SQ SN:0 LN:53 591s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 591s 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 591s matchesRef regression 2 (fw:1, sam:1) 591s References: 591s >0 591s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 591s >1 591s CCTTGTTNTTAATGCTGCCTGGTTTNG 591s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 592s /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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 592s @HD VN:1.5 SO:unsorted GO:query 592s @SQ SN:0 LN:47 592s @SQ SN:1 LN:27 592s @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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 592s r0 77 * 0 0 * * 0 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 592s r0 141 * 0 0 * * 0 0 ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 592s matchesRef regression 2 (fw:0, sam:1) 592s References: 592s >0 592s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 592s >1 592s CCTTGTTNTTAATGCTGCCTGGTTTNG 592s /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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 592s @HD VN:1.5 SO:unsorted GO:query 592s @SQ SN:0 LN:47 592s @SQ SN:1 LN:27 592s @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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 592s 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 592s 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 592s matchesRef regression 1 (fw:1, sam:1) 592s References: 592s >0 592s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 592s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 593s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 593s @HD VN:1.5 SO:unsorted GO:query 593s @SQ SN:0 LN:61 593s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 593s 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 593s matchesRef regression 1 (fw:0, sam:1) 593s References: 593s >0 593s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 593s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 594s @HD VN:1.5 SO:unsorted GO:query 594s @SQ SN:0 LN:61 594s @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" 594s 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 594s Discordant with different chromosomes (fw:1, sam:1) 594s References: 594s >0 594s TTTATAAAAATATTTCCCCCCCC 594s >1 594s CCCCCCTGTCGCTACCGCCCCCCCCCCC 594s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 594s /usr/bin/bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 12 -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 595s @HD VN:1.5 SO:unsorted GO:query 595s @SQ SN:0 LN:23 595s @SQ SN:1 LN:28 595s @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 12 -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" 595s 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 595s 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 595s 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 595s 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 595s Discordant with different chromosomes (fw:0, sam:1) 595s References: 595s >0 595s TTTATAAAAATATTTCCCCCCCC 595s >1 595s CCCCCCTGTCGCTACCGCCCCCCCCCCC 595s /usr/bin/bowtie2 -I 0 -X 35 --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 595s @HD VN:1.5 SO:unsorted GO:query 595s @SQ SN:0 LN:23 595s @SQ SN:1 LN:28 595s @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 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" 595s 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 595s 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 595s 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 595s 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 595s (fw:1, sam:1) 595s References: 595s >0 595s AGCATCGATCAGTATCTGA 595s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 596s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.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-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 596s 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 596s (fw:0, sam:1) 596s References: 596s >0 596s AGCATCGATCAGTATCTGA 596s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.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-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 596s 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 596s (fw:1, sam:1) 596s References: 596s >0 596s AGCATCGATCAGTATCTGA 596s /usr/bin/bowtie2 -s 1 --fr --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 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-s --wrapper basic-0 -s 1 --fr --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" 597s 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 597s 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 597s (fw:0, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /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 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-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" 597s 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 597s 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 597s (fw:1, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /usr/bin/bowtie2 -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.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-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 597s (fw:0, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /usr/bin/bowtie2 -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.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-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 598s (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAGTATCTGA 598s /usr/bin/bowtie2 -s 2 --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 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-s --wrapper basic-0 -s 2 --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" 598s (fw:0, sam:1) 598s References: 598s >0 598s AGCATCGATCAGTATCTGA 598s /usr/bin/bowtie2 -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 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-s --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" 598s (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAGTATCTGA 598s /usr/bin/bowtie2 -s 1 -u 1 --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 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-s --wrapper basic-0 -s 1 -u 1 --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" 598s 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 598s (fw:0, sam:1) 598s References: 598s >0 598s AGCATCGATCAGTATCTGA 598s /usr/bin/bowtie2 -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 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-s --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" 598s 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 598s (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAGTATCTGA 598s /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 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-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" 599s 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 599s (fw:0, sam:1) 599s References: 599s >0 599s AGCATCGATCAGTATCTGA 599s /usr/bin/bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.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-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 599s 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 599s (fw:0, sam:1) 599s References: 599s >0 599s AGCATCGATCAGTATCTGA 599s /usr/bin/bowtie2 -s 1 --trim5 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.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-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 599s 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 599s (fw:1, sam:1) 599s References: 599s >0 599s AGCATCGATCAGTATCTGA 599s /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 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-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" 600s 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 600s (fw:1, sam:1) 600s References: 600s >0 600s TGC 600s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 600s /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 601s @HD VN:1.5 SO:unsorted GO:query 601s @SQ SN:0 LN:3 601s @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" 601s 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 601s (fw:0, sam:1) 601s References: 601s >0 601s TGC 601s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 601s @HD VN:1.5 SO:unsorted GO:query 601s @SQ SN:0 LN:3 601s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 601s 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 601s (fw:1, sam:1) 601s References: 601s >0 601s TTGTTCGT 601s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 602s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 602s @HD VN:1.5 SO:unsorted GO:query 602s @SQ SN:0 LN:8 602s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 602s 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 602s (fw:0, sam:1) 602s References: 602s >0 602s TTGTTCGT 602s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 602s @HD VN:1.5 SO:unsorted GO:query 602s @SQ SN:0 LN:8 602s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 602s 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 602s (fw:1, sam:1) 602s References: 602s >0 602s TTGTTCGT 602s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 602s @HD VN:1.5 SO:unsorted GO:query 602s @SQ SN:0 LN:8 602s @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.1a.fq.gz" 602s 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 602s (fw:0, sam:1) 602s References: 602s >0 602s TTGTTCGT 602s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 602s @HD VN:1.5 SO:unsorted GO:query 602s @SQ SN:0 LN:8 602s @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 .simple_tests.1a.fq.gz" 602s 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 602s (fw:1, sam:1) 602s References: 602s >0 602s TTGTTCGT 603s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 603s @HD VN:1.5 SO:unsorted GO:query 603s @SQ SN:0 LN:8 603s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 603s 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 603s 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 603s (fw:0, sam:1) 603s References: 603s >0 603s TTGTTCGT 603s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 603s @HD VN:1.5 SO:unsorted GO:query 603s @SQ SN:0 LN:8 603s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 603s 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 603s 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 603s (fw:1, sam:1) 603s References: 603s >0 603s TTGTTCGT 603s /usr/bin/bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 603s @HD VN:1.5 SO:unsorted GO:query 603s @SQ SN:0 LN:8 603s @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 -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 603s 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 603s 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 603s (fw:0, sam:1) 603s References: 603s >0 603s TTGTTCGT 603s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 603s @HD VN:1.5 SO:unsorted GO:query 603s @SQ SN:0 LN:8 603s @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" 603s 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 603s 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 603s (fw:1, sam:1) 603s References: 603s >0 603s TTGTTCGT 603s /usr/bin/bowtie2 --overhang --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 604s @HD VN:1.5 SO:unsorted GO:query 604s @SQ SN:0 LN:8 604s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 604s 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 604s 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 604s 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 604s (fw:0, sam:1) 604s References: 604s >0 604s TTGTTCGT 604s /usr/bin/bowtie2 --overhang --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 604s @HD VN:1.5 SO:unsorted GO:query 604s @SQ SN:0 LN:8 604s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 604s 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 604s 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 604s 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 604s (fw:1, sam:1) 604s References: 604s >0 604s TTGTTCGT 604s /usr/bin/bowtie2 --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 604s @HD VN:1.5 SO:unsorted GO:query 604s @SQ SN:0 LN:8 604s @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 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" 604s 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 604s 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 604s r2 4 * 0 0 * * 0 0 GTTCGTA IIIIIII YT:Z:UU 604s r3 4 * 0 0 * * 0 0 ATTGTTC IIIIIII YT:Z:UU 604s (fw:0, sam:1) 604s References: 604s >0 604s TTGTTCGT 604s /usr/bin/bowtie2 --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,.simple_tests.1d.fq.gz 604s @HD VN:1.5 SO:unsorted GO:query 604s @SQ SN:0 LN:8 604s @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 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" 604s 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 604s 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 604s r2 4 * 0 0 * * 0 0 TACGAAC IIIIIII YT:Z:UU 604s r3 4 * 0 0 * * 0 0 GAACAAT IIIIIII YT:Z:UU 604s (fw:1, sam:1) 604s References: 604s >0 604s TTGTTCGT 604s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 605s @HD VN:1.5 SO:unsorted GO:query 605s @SQ SN:0 LN:8 605s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 605s 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 605s (fw:0, sam:1) 605s References: 605s >0 605s TTGTTCGT 605s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 605s @HD VN:1.5 SO:unsorted GO:query 605s @SQ SN:0 LN:8 605s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 605s 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 605s (fw:1, sam:1) 605s References: 605s >0 605s TTGTTCGT 605s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 605s @HD VN:1.5 SO:unsorted GO:query 605s @SQ SN:0 LN:8 605s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 605s 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 605s (fw:0, sam:1) 605s References: 605s >0 605s TTGTTCGT 605s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 605s @HD VN:1.5 SO:unsorted GO:query 605s @SQ SN:0 LN:8 605s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 605s 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 605s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 605s References: 605s >0 605s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 605s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 606s /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 606s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:1000 606s @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" 606s 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 606s 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 606s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 606s References: 606s >0 606s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 606s /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 606s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:1000 606s @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" 606s 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 606s 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 606s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 606s References: 606s >0 606s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 607s /usr/bin/bowtie2 -X 1000 --local --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 607s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 607s @HD VN:1.5 SO:unsorted GO:query 607s @SQ SN:0 LN:1000 607s @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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 607s 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 607s 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 607s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 607s References: 607s >0 607s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 607s /usr/bin/bowtie2 -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 607s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 607s @HD VN:1.5 SO:unsorted GO:query 607s @SQ SN:0 LN:1000 607s @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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 607s 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 607s 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 607s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 607s References: 607s >0 607s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 607s /usr/bin/bowtie2 -X 1000 --fr --quiet -k 5 --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:1000 607s @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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 607s 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 607s 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 607s 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 607s 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 607s 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 607s 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 607s 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 607s 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 607s 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 607s 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 607s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 607s References: 607s >0 607s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 607s /usr/bin/bowtie2 -X 1000 --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 607s @HD VN:1.5 SO:unsorted GO:query 607s @SQ SN:0 LN:1000 607s @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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 607s 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 607s 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 607s 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 607s 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 607s 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 607s 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 607s 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 607s 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 607s 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 607s 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 607s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 607s References: 607s >0 607s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 607s /usr/bin/bowtie2 -X 1000 --local --fr --quiet -k 5 --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:1000 608s @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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 608s 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 608s 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 608s 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 608s 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 608s 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 608s 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 608s 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 608s 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 608s 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 608s 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 608s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 608s References: 608s >0 608s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 608s /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 608s @HD VN:1.5 SO:unsorted GO:query 608s @SQ SN:0 LN:1000 608s @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" 608s 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 608s 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 608s 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 608s 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 608s 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 608s 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 608s 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 608s 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 608s 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 608s 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 608s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 608s References: 608s >0 608s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 608s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 609s /usr/bin/bowtie2 -X 150 --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 609s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 609s @HD VN:1.5 SO:unsorted GO:query 609s @SQ SN:0 LN:363 609s @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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 609s 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 609s 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 609s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 609s References: 609s >0 609s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 609s /usr/bin/bowtie2 -X 150 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 609s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 609s @HD VN:1.5 SO:unsorted GO:query 609s @SQ SN:0 LN:363 609s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 609s 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 609s 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 609s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 609s References: 609s >0 609s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 609s /usr/bin/bowtie2 --local -X 150 --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 609s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 609s @HD VN:1.5 SO:unsorted GO:query 609s @SQ SN:0 LN:363 609s @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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 609s 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 609s 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 609s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 609s References: 609s >0 609s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 609s /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 610s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 610s @HD VN:1.5 SO:unsorted GO:query 610s @SQ SN:0 LN:363 610s @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" 610s 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 610s 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 610s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 610s References: 610s >0 610s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 610s /usr/bin/bowtie2 -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 610s @HD VN:1.5 SO:unsorted GO:query 610s @SQ SN:0 LN:363 610s @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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 610s 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 610s 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 610s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 610s References: 610s >0 610s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 610s /usr/bin/bowtie2 -X 150 --fr --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 610s @HD VN:1.5 SO:unsorted GO:query 610s @SQ SN:0 LN:363 610s @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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 610s 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 610s 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 610s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 610s References: 610s >0 610s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 610s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 610s @HD VN:1.5 SO:unsorted GO:query 610s @SQ SN:0 LN:363 610s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 610s 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 610s 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 610s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 610s References: 610s >0 610s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 610s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 611s @HD VN:1.5 SO:unsorted GO:query 611s @SQ SN:0 LN:363 611s @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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 611s 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 611s 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 611s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 611s References: 611s >0 611s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 611s /usr/bin/bowtie2 --fr --quiet -M 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 611s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 611s @HD VN:1.5 SO:unsorted GO:query 611s @SQ SN:0 LN:363 611s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 611s 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 611s 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 611s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 611s References: 611s >0 611s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 611s /usr/bin/bowtie2 --fr --quiet -M 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 611s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 611s @HD VN:1.5 SO:unsorted GO:query 611s @SQ SN:0 LN:363 611s @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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 611s 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 611s 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 611s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 611s References: 611s >0 611s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 611s /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 611s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 611s @HD VN:1.5 SO:unsorted GO:query 611s @SQ SN:0 LN:363 611s @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" 611s 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 611s 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 611s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 611s References: 611s >0 611s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 611s /usr/bin/bowtie2 --fr --quiet -M 1 --local -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 612s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 612s @HD VN:1.5 SO:unsorted GO:query 612s @SQ SN:0 LN:363 612s @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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 612s 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 612s 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 612s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 612s References: 612s >0 612s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 612s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 612s /usr/bin/bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 613s @HD VN:1.5 SO:unsorted GO:query 613s @SQ SN:0 LN:126 613s @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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 613s 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 613s 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 613s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 613s References: 613s >0 613s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 613s /usr/bin/bowtie2 --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 613s @HD VN:1.5 SO:unsorted GO:query 613s @SQ SN:0 LN:126 613s @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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 613s 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 613s 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 613s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 613s References: 613s >0 613s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 613s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 613s @HD VN:1.5 SO:unsorted GO:query 613s @SQ SN:0 LN:126 613s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 613s 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 613s 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 613s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 613s References: 613s >0 613s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 613s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 613s @HD VN:1.5 SO:unsorted GO:query 613s @SQ SN:0 LN:126 613s @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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 613s 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 613s 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 613s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 613s References: 613s >0 613s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 613s /usr/bin/bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.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:126 614s @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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 614s 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 614s 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 614s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 614s References: 614s >0 614s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 614s /usr/bin/bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.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:126 614s @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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 614s 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 614s 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 614s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 614s References: 614s >0 614s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 614s /usr/bin/bowtie2 -X 150 --local --fr --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.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:126 614s @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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 614s 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 614s 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 614s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 614s References: 614s >0 614s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 614s /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 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:126 614s @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" 614s 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 614s 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 614s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 614s References: 614s >0 614s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 614s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 615s /usr/bin/bowtie2 -X 150 --fr --quiet -M 5 --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:2607 615s @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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 615s 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 615s 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 615s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 615s References: 615s >0 615s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 615s /usr/bin/bowtie2 -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 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:2607 616s @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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 616s 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 616s 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 616s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:1, sam:1) 616s References: 616s >0 616s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 616s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 616s /usr/bin/bowtie2 --local -X 150 --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 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:1906 617s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 617s 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 617s 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 617s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1) 617s References: 617s >0 617s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 617s /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 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:1906 617s @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" 617s 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 617s 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 617s U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1) 617s References: 617s >0 617s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 617s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 618s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 9 -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:56 618s @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" 618s 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 618s U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1) 618s References: 618s >0 618s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 618s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 2 -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:56 618s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 618s 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 618s U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1) 618s References: 618s >0 618s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 618s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 2 -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:56 618s @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" 618s 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 618s U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1) 618s References: 618s >0 618s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 618s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 12 -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:56 618s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 618s 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 618s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1) 618s References: 618s >0 618s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 618s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:56 619s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s 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 619s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1) 619s References: 619s >0 619s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 619s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:56 619s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s 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 619s U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1) 619s References: 619s >0 619s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 619s /usr/bin/bowtie2 --local --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:56 619s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s 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 619s U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1) 619s References: 619s >0 619s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 619s /usr/bin/bowtie2 --local --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:56 619s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s 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 619s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1) 619s References: 619s >0 619s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 619s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 620s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 12 -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:85 620s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 620s 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 620s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1) 620s References: 620s >0 620s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 620s /usr/bin/bowtie2 --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. 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:85 621s @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" 621s 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 621s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1) 621s References: 621s >0 621s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 621s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 2 -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:85 621s @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" 621s 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 621s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) 621s References: 621s >0 621s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 621s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 9 -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:85 621s @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" 621s 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 621s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1) 621s References: 621s >0 621s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 621s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:85 621s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 621s 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 621s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) 621s References: 621s >0 621s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 621s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:85 621s @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" 621s 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 621s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1) 621s References: 621s >0 621s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 621s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 622s @HD VN:1.5 SO:unsorted GO:query 622s @SQ SN:0 LN:85 622s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 622s 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 622s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) 622s References: 622s >0 622s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 622s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 622s @HD VN:1.5 SO:unsorted GO:query 622s @SQ SN:0 LN:85 622s @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" 622s 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 622s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1) 622s References: 622s >0 622s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 622s /usr/bin/bowtie2 --quiet -M 2 --reads-per-batch 16 -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:85 622s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 622s 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 622s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1) 622s References: 622s >0 622s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 622s /usr/bin/bowtie2 --quiet -M 2 --reads-per-batch 6 -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:85 622s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 622s 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 622s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1) 622s References: 622s >0 622s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 622s /usr/bin/bowtie2 --quiet -M 2 --local --reads-per-batch 13 -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:85 623s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 623s 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 623s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1) 623s References: 623s >0 623s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 623s /usr/bin/bowtie2 --quiet -M 2 --local --reads-per-batch 8 -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:85 623s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 623s 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 623s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1) 623s References: 623s >0 623s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 623s /usr/bin/bowtie2 --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 623s @HD VN:1.5 SO:unsorted GO:query 623s @SQ SN:0 LN:85 623s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 623s 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 623s 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 623s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1) 623s References: 623s >0 623s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 623s /usr/bin/bowtie2 --quiet -k 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 623s @HD VN:1.5 SO:unsorted GO:query 623s @SQ SN:0 LN:85 623s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 623s 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 623s 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 623s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1) 623s References: 623s >0 623s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 623s /usr/bin/bowtie2 --local --quiet -k 2 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 623s @HD VN:1.5 SO:unsorted GO:query 623s @SQ SN:0 LN:85 623s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 623s 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 623s 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 623s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1) 623s References: 623s >0 623s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 624s /usr/bin/bowtie2 --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 624s @HD VN:1.5 SO:unsorted GO:query 624s @SQ SN:0 LN:85 624s @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" 624s 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 624s 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 624s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 624s References: 624s >0 624s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 624s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 624s /usr/bin/bowtie2 -X 150 --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 625s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 625s @HD VN:1.5 SO:unsorted GO:query 625s @SQ SN:0 LN:340 625s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 625s 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 625s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 625s References: 625s >0 625s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 625s /usr/bin/bowtie2 -X 150 --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 625s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 625s @HD VN:1.5 SO:unsorted GO:query 625s @SQ SN:0 LN:340 625s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 625s 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 625s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 625s References: 625s >0 625s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 625s /usr/bin/bowtie2 --local --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 625s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 625s @HD VN:1.5 SO:unsorted GO:query 625s @SQ SN:0 LN:340 625s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 625s 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 625s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 625s References: 625s >0 625s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 625s /usr/bin/bowtie2 --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 625s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 625s @HD VN:1.5 SO:unsorted GO:query 625s @SQ SN:0 LN:340 625s @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" 625s 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 625s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1) 625s References: 625s >0 625s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 625s /usr/bin/bowtie2 --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:340 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s 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 626s 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 626s 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 626s 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 626s 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 626s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:0, sam:1) 626s References: 626s >0 626s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 626s /usr/bin/bowtie2 --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:340 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s 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 626s 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 626s 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 626s 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 626s 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 626s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:1, sam:1) 626s References: 626s >0 626s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 626s /usr/bin/bowtie2 --local --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:340 626s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s 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 626s 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 626s 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 626s 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 626s 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 626s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:0, sam:1) 626s References: 626s >0 626s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 626s /usr/bin/bowtie2 --local --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:340 626s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s 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 626s 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 626s 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 626s 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 626s 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 626s (fw:1, sam:1) 626s References: 626s >0 626s TTGTTCGTTTGTTCGT 626s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 627s /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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 627s @HD VN:1.5 SO:unsorted GO:query 627s @SQ SN:0 LN:16 627s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 627s 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 627s 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 627s (fw:0, sam:1) 627s References: 627s >0 627s TTGTTCGTTTGTTCGT 627s /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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:16 628s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s 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 628s 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 628s (fw:1, sam:1) 628s References: 628s >0 628s TTGTTCGTTTGTTCGT 628s /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 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:16 628s @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" 628s r0 4 * 0 0 * * 0 0 TTGTTCAT IIIIIIII YT:Z:UU 628s (fw:0, sam:1) 628s References: 628s >0 628s TTGTTCGTTTGTTCGT 628s /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 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:16 628s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU 628s (fw:1, sam:1) 628s References: 628s >0 628s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 628s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 629s /usr/bin/bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 10 -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 629s @HD VN:1.5 SO:unsorted GO:query 629s @SQ SN:0 LN:49 629s @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 10 -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" 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s (fw:0, sam:1) 629s References: 629s >0 629s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 629s /usr/bin/bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 13 -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 629s @HD VN:1.5 SO:unsorted GO:query 629s @SQ SN:0 LN:49 629s @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 13 -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" 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s 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 629s Gap penalties 1 (fw:1, sam:1) 629s References: 629s >0 629s TTGTTCGTTTGTTCGT 629s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 630s /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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 630s @HD VN:1.5 SO:unsorted GO:query 630s @SQ SN:0 LN:16 630s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 630s 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 630s Gap penalties 1 (fw:0, sam:1) 630s References: 630s >0 630s TTGTTCGTTTGTTCGT 630s /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 631s @HD VN:1.5 SO:unsorted GO:query 631s @SQ SN:0 LN:16 631s @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" 631s 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 631s Gap penalties 2 (fw:1, sam:1) 631s References: 631s >0 631s TTGTTCGTTTGTTCGT 631s /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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 631s @HD VN:1.5 SO:unsorted GO:query 631s @SQ SN:0 LN:16 631s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 631s r0 4 * 0 0 * * 0 0 TTGTTCTTTGTT IIIIIIIIIIII YT:Z:UU 631s Gap penalties 2 (fw:0, sam:1) 631s References: 631s >0 631s TTGTTCGTTTGTTCGT 631s /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 631s @HD VN:1.5 SO:unsorted GO:query 631s @SQ SN:0 LN:16 631s @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" 631s r0 4 * 0 0 * * 0 0 AACAAAGAACAA IIIIIIIIIIII YT:Z:UU 631s Gap penalties 3 (fw:1, sam:1) 631s References: 631s >0 631s TTGTTCGTTTGTTCGT 631s /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 631s @HD VN:1.5 SO:unsorted GO:query 631s @SQ SN:0 LN:16 631s @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" 631s 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 631s Gap penalties 3 (fw:0, sam:1) 631s References: 631s >0 631s TTGTTCGTTTGTTCGT 631s /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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 632s @HD VN:1.5 SO:unsorted GO:query 632s @SQ SN:0 LN:16 632s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 632s 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 632s Gap penalties 4 (fw:1, sam:1) 632s References: 632s >0 632s TTGTTCGTTTGTTCGT 632s /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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 632s @HD VN:1.5 SO:unsorted GO:query 632s @SQ SN:0 LN:16 632s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 632s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 632s Gap penalties 4 (fw:0, sam:1) 632s References: 632s >0 632s TTGTTCGTTTGTTCGT 632s /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 632s @HD VN:1.5 SO:unsorted GO:query 632s @SQ SN:0 LN:16 632s @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" 632s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 632s Gap penalties 5 (fw:1, sam:1) 632s References: 632s >0 632s TTGTTCGTTTGTTCGT 632s /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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 632s @HD VN:1.5 SO:unsorted GO:query 632s @SQ SN:0 LN:16 632s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 632s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 632s Gap penalties 5 (fw:0, sam:1) 632s References: 632s >0 632s TTGTTCGTTTGTTCGT 632s /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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:16 633s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 633s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 633s Gap penalties 6 (fw:1, sam:1) 633s References: 633s >0 633s ATTGTTCGTTTGTTCGTA 633s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 633s /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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:18 634s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 634s 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 634s Gap penalties 6 (fw:0, sam:1) 634s References: 634s >0 634s ATTGTTCGTTTGTTCGTA 634s /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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:18 634s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 634s 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 634s Gap penalties 7 (fw:1, sam:1) 634s References: 634s >0 634s TTGTTCGTTTGTTCGT 634s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 635s /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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 635s @HD VN:1.5 SO:unsorted GO:query 635s @SQ SN:0 LN:16 635s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 635s r0 4 * 0 0 * * 0 0 TTGTTGTTTGATTCGT IIIIIIIIIIIIIIII YT:Z:UU 635s Gap penalties 7 (fw:0, sam:1) 635s References: 635s >0 635s TTGTTCGTTTGTTCGT 635s /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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 635s @HD VN:1.5 SO:unsorted GO:query 635s @SQ SN:0 LN:16 635s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 635s r0 4 * 0 0 * * 0 0 ACGAATCAAACAACAA IIIIIIIIIIIIIIII YT:Z:UU 635s N filtering 1 (fw:1, sam:1) 635s References: 635s >0 635s GAGACTTTATACGCATCGAACTATCGCTCTA 635s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 636s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 636s @HD VN:1.5 SO:unsorted GO:query 636s @SQ SN:0 LN:31 636s @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" 636s 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 636s N filtering 1 (fw:0, sam:1) 636s References: 636s >0 636s GAGACTTTATACGCATCGAACTATCGCTCTA 636s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --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:31 636s @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" 636s 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 636s N filtering 2 (fw:1, sam:1) 636s References: 636s >0 636s GAGACTTTATNCGCATCGAACTATCGCTCTA 636s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 637s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 637s @HD VN:1.5 SO:unsorted GO:query 637s @SQ SN:0 LN:31 637s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 637s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 637s N filtering 2 (fw:0, sam:1) 637s References: 637s >0 637s GAGACTTTATNCGCATCGAACTATCGCTCTA 637s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 638s @HD VN:1.5 SO:unsorted GO:query 638s @SQ SN:0 LN:31 638s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 638s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 638s N filtering 3 (fw:1, sam:1) 638s References: 638s >0 638s GAGACTTTATACGCATCGAANTATCGCTCTA 638s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 638s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 639s @HD VN:1.5 SO:unsorted GO:query 639s @SQ SN:0 LN:31 639s @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" 639s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 639s N filtering 3 (fw:0, sam:1) 639s References: 639s >0 639s GAGACTTTATACGCATCGAANTATCGCTCTA 639s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 639s @HD VN:1.5 SO:unsorted GO:query 639s @SQ SN:0 LN:31 639s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 639s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 639s N filtering 4 (fw:1, sam:1) 639s References: 639s >0 639s GAGACTTTNTACGCATCGAACTATCGCTCTA 639s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 639s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 640s @HD VN:1.5 SO:unsorted GO:query 640s @SQ SN:0 LN:31 640s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 640s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 640s N filtering 4 (fw:0, sam:1) 640s References: 640s >0 640s GAGACTTTNTACGCATCGAACTATCGCTCTA 640s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 640s @HD VN:1.5 SO:unsorted GO:query 640s @SQ SN:0 LN:31 640s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 640s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 640s N filtering 5 (fw:1, sam:1) 640s References: 640s >0 640s GAGACTTTATNCGCATCGAACTATCGCTCTA 640s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 641s /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 641s @HD VN:1.5 SO:unsorted GO:query 641s @SQ SN:0 LN:31 641s @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" 641s 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 641s N filtering 5 (fw:0, sam:1) 641s References: 641s >0 641s GAGACTTTATNCGCATCGAACTATCGCTCTA 641s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --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:31 641s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 641s 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 641s N filtering 6 (fw:1, sam:1) 641s References: 641s >0 641s GAGACTTTNTACGCATCGAANTATCGCTCTA 641s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 642s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:31 642s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 642s N filtering 6 (fw:0, sam:1) 642s References: 642s >0 642s GAGACTTTNTACGCATCGAANTATCGCTCTA 642s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:31 642s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 642s (fw:1, sam:1) 642s References: 642s >0 642s TTTTGTTCGTTTG 642s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 643s /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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 644s @HD VN:1.5 SO:unsorted GO:query 644s @SQ SN:0 LN:13 644s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 644s 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 644s (fw:0, sam:1) 644s References: 644s >0 644s TTTTGTTCGTTTG 644s /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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 644s @HD VN:1.5 SO:unsorted GO:query 644s @SQ SN:0 LN:13 644s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 644s 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 644s (fw:1, sam:1) 644s References: 644s >0 644s TTGTTCGTTTGTT 644s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 645s /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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 645s @HD VN:1.5 SO:unsorted GO:query 645s @SQ SN:0 LN:13 645s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 645s 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 645s (fw:0, sam:1) 645s References: 645s >0 645s TTGTTCGTTTGTT 645s /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 645s @HD VN:1.5 SO:unsorted GO:query 645s @SQ SN:0 LN:13 645s @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" 645s 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 645s (fw:1, sam:1) 645s References: 645s >0 645s ACNCA 645s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 646s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 646s @HD VN:1.5 SO:unsorted GO:query 646s @SQ SN:0 LN:5 646s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 646s 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 646s (fw:0, sam:1) 646s References: 646s >0 646s ACNCA 646s /usr/bin/bowtie2 --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 646s @HD VN:1.5 SO:unsorted GO:query 646s @SQ SN:0 LN:5 646s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 646s 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 647s N ceil = 0, 2 legit hits (1) (fw:1, sam:1) 647s References: 647s >0 647s ACNCA 647s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --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:5 647s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s 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 647s N ceil = 0, 2 legit hits (1) (fw:0, sam:1) 647s References: 647s >0 647s ACNCA 647s /usr/bin/bowtie2 --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 647s @HD VN:1.5 SO:unsorted GO:query 647s @SQ SN:0 LN:5 647s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s 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 647s N ceil = 0, 2 legit hits (2) (fw:1, sam:1) 647s References: 647s >0 647s ACNCANNNNNNNNCGNNNNNNNNCG 647s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 648s /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 648s @HD VN:1.5 SO:unsorted GO:query 648s @SQ SN:0 LN:25 648s @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" 648s 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 648s 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 648s 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 648s 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 648s N ceil = 0, 2 legit hits (2) (fw:0, sam:1) 648s References: 648s >0 648s ACNCANNNNNNNNCGNNNNNNNNCG 648s /usr/bin/bowtie2 --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 648s @HD VN:1.5 SO:unsorted GO:query 648s @SQ SN:0 LN:25 648s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 648s 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 648s 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 648s 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 648s 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 648s (fw:1, sam:1) 648s References: 648s >0 648s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 648s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 649s /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 649s @HD VN:1.5 SO:unsorted GO:query 649s @SQ SN:0 LN:37 649s @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" 649s 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 649s 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 649s 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 649s 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 649s 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 649s 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 649s (fw:0, sam:1) 649s References: 649s >0 649s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 649s /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 650s @HD VN:1.5 SO:unsorted GO:query 650s @SQ SN:0 LN:37 650s @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" 650s 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 650s 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 650s 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 650s 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 650s 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 650s 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 650s (fw:1, sam:1) 650s References: 650s >0 650s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 650s /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 650s @HD VN:1.5 SO:unsorted GO:query 650s @SQ SN:0 LN:37 650s @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" 650s 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 650s 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 650s 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 650s 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 650s 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 650s 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 650s (fw:0, sam:1) 650s References: 650s >0 650s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 650s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 650s @HD VN:1.5 SO:unsorted GO:query 650s @SQ SN:0 LN:37 650s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 650s 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 650s 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 650s 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 650s 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 650s 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 650s 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 650s (fw:1, sam:1) 650s References: 650s >0 650s TTGTTYGT 650s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 651s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 651s @HD VN:1.5 SO:unsorted GO:query 651s @SQ SN:0 LN:8 651s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 651s 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 651s 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 651s (fw:1, sam:1) 651s References: 651s >0 651s ATAACCTTCG 651s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 652s /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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 652s @HD VN:1.5 SO:unsorted GO:query 652s @SQ SN:0 LN:10 652s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 652s 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 652s (fw:0, sam:1) 652s References: 652s >0 652s ATAACCTTCG 652s /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 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-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" 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 --quiet .simple_tests.pl.fa .simple_tests.tmp 653s /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 3 -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-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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 654s 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 654s (fw:1, sam:1) 654s References: 654s >0 654s ATATGCCCCATGCCCCCCTCCG 654s /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 15 -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-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 15 -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 --quiet .simple_tests.pl.fa .simple_tests.tmp 655s /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 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-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" 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 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 655s 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 655s 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 655s 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 655s 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 655s 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 655s 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 655s 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 655s 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 655s 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 655s 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 655s 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 655s 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 655s 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 655s 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 655s Simple paired-end 13 (fw:0, sam:1) 655s References: 655s >0 655s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 655s /usr/bin/bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 2 -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 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:51 656s @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 2 -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" 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s 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 656s Simple paired-end 12 (fw:1, sam:1) 656s References: 656s >0 656s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 656s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 657s /usr/bin/bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -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 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:51 657s @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 15 -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" 657s 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 657s 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 657s 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 657s 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 657s Simple paired-end 12 (fw:0, sam:1) 657s References: 657s >0 657s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 657s /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,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:51 657s @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,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 657s 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 657s 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 657s 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 657s 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 657s Simple paired-end 11 (fw:1, sam:1) 657s References: 657s >0 657s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 657s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 658s /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 -2 .simple_tests.2a.fq.gz 658s @HD VN:1.5 SO:unsorted GO:query 658s @SQ SN:0 LN:51 658s @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 -2 .simple_tests.2a.fq.gz" 658s 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 658s 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 658s Simple paired-end 11 (fw:0, sam:1) 658s References: 658s >0 658s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 658s /usr/bin/bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -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:51 658s @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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 658s 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 658s 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 658s Simple paired-end 10 (fw:1, sam:1) 658s References: 658s >0 658s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 658s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 659s /usr/bin/bowtie2 -I 28 -X 80 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:41 659s @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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 659s 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 659s 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 659s Simple paired-end 10 (fw:0, sam:1) 659s References: 659s >0 659s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 659s /usr/bin/bowtie2 -I 28 -X 80 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:41 660s @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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 660s 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 660s 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 660s Simple paired-end 9 (fw:1, sam:1) 660s References: 660s >0 660s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 660s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 660s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 661s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 661s @HD VN:1.5 SO:unsorted GO:query 661s @SQ SN:0 LN:81 661s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 661s 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 661s 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 661s Simple paired-end 9 (fw:0, sam:1) 661s References: 661s >0 661s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 661s /usr/bin/bowtie2 -I 0 -X 80 --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 661s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 661s @HD VN:1.5 SO:unsorted GO:query 661s @SQ SN:0 LN:81 661s @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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 661s 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 661s 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 661s Simple paired-end 8 (fw:1, sam:1) 661s References: 661s >0 661s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 661s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 662s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:81 662s @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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 662s 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 662s 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 662s 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 662s 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 662s 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 662s 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 662s Simple paired-end 8 (fw:0, sam:1) 662s References: 662s >0 662s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 662s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:81 662s @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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 662s 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 662s 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 662s 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 662s 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 662s 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 662s 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 662s Simple paired-end 2; no --no-mixed (fw:0, sam:1) 662s References: 662s >0 662s CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC 662s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 663s /usr/bin/bowtie2 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:53 663s @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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 663s 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 663s r0 101 0 4 0 * = 4 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 663s Simple paired-end 2; --no-mixed (fw:1, sam:1) 663s References: 663s >0 663s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 663s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 664s /usr/bin/bowtie2 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 664s @HD VN:1.5 SO:unsorted GO:query 664s @SQ SN:0 LN:53 664s @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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 664s r0 77 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 664s r0 141 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 665s Simple paired-end 2; --no-mixed (fw:0, sam:1) 665s References: 665s >0 665s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 665s /usr/bin/bowtie2 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 665s @HD VN:1.5 SO:unsorted GO:query 665s @SQ SN:0 LN:53 665s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 665s r0 77 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 665s r0 141 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 665s Simple paired-end 1 (fw:1, sam:1) 665s References: 665s >0 665s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 665s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 666s /usr/bin/bowtie2 -I 0 -X 50 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:53 666s @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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 666s 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 666s 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 666s Simple paired-end 1 (fw:0, sam:1) 666s References: 666s >0 666s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 666s /usr/bin/bowtie2 -I 0 -X 50 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:53 666s @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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 666s 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 666s 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 666s (fw:1, sam:1) 666s References: 666s >0 666s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 666s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 667s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 12 -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 667s @HD VN:1.5 SO:unsorted GO:query 667s @SQ SN:0 LN:49 667s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -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" 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s 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 667s (fw:0, sam:1) 667s References: 667s >0 667s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 667s /usr/bin/bowtie2 --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 668s @HD VN:1.5 SO:unsorted GO:query 668s @SQ SN:0 LN:49 668s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --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" 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s 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 668s (fw:1, sam:1) 668s References: 668s >0 668s TTGTTCGTTTGTTCGT 668s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 668s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:16 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s 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 669s (fw:0, sam:1) 669s References: 669s >0 669s TTGTTCGTTTGTTCGT 669s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:16 669s @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" 669s 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 669s (fw:1, sam:1) 669s References: 669s >0 669s TTGTTCGT 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 670s /usr/bin/bowtie2 --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 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:8 670s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 670s 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 670s (fw:0, sam:1) 670s References: 670s >0 670s TTGTTCGT 670s /usr/bin/bowtie2 --overhang --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 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:8 670s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 670s 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 670s (fw:1, sam:1) 670s References: 670s >0 670s TTGTTCGTTTGTTCGT 670s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 671s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:16 671s @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" 671s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 671s (fw:0, sam:1) 671s References: 671s >0 671s TTGTTCGTTTGTTCGT 671s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:16 672s @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" 672s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 672s (fw:1, sam:1) 672s References: 672s >0 672s TTGTTCGTTTGTTCGT 672s /usr/bin/bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:16 672s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 672s (fw:0, sam:1) 672s References: 672s >0 672s TTGTTCGTTTGTTCGT 672s /usr/bin/bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:16 672s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 672s (fw:1, sam:1) 672s References: 672s >0 672s TTGTTCGTTTGTTCGT 672s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:16 672s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 672s (fw:0, sam:1) 672s References: 672s >0 672s TTGTTCGTTTGTTCGT 672s /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 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @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" 673s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 673s (fw:1, sam:1) 673s References: 673s >0 673s TTGTTCGTTTGTTCGT 673s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s 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 673s 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 673s 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 673s 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 673s 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 673s 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 673s (fw:0, sam:1) 673s References: 673s >0 673s TTGTTCGTTTGTTCGT 673s /usr/bin/bowtie2 --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 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s 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 673s 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 673s 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 673s 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 673s 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 673s 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 673s FASTA-continuous 1 (fw:1, sam:1) 673s References: 673s >0 673s AGCATCGATCAGTATCTGA 673s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 674s /usr/bin/bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp .simple_tests.gz 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:19 674s @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 11 -x .simple_tests.tmp .simple_tests.gz" 674s 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 674s 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 674s FASTA-continuous 2 (fw:1, sam:1) 674s References: 674s >0 674s AGCATCGATCAGTATCTGA 674s /usr/bin/bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp .simple_tests.gz 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:19 675s @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 5 -x .simple_tests.tmp .simple_tests.gz" 675s 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 675s 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 675s 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 675s FASTA-continuous 3 (fw:1, sam:1) 675s References: 675s >0 675s AGCATCGATCAGTATCTGA 675s /usr/bin/bowtie2 --large-index -F 10,9 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:19 675s @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 4 -x .simple_tests.tmp .simple_tests.gz" 675s 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 675s FASTA-continuous 4 (fw:1, sam:1) 675s References: 675s >0 675s AGCATCGATCAGTATCTGA 675s /usr/bin/bowtie2 --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:19 675s @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 13 -x .simple_tests.tmp .simple_tests.gz" 675s 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 675s FASTA-continuous 5 (fw:1, sam:1) 675s References: 675s >0 675s AGCATCGATCAGTATCTGA 675s /usr/bin/bowtie2 --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:19 675s @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 6 -x .simple_tests.tmp .simple_tests.gz" 675s 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 675s FASTA-continuous 6 (fw:1, sam:1) 675s References: 675s >0 675s AGCATCGATCAG 675s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 676s /usr/bin/bowtie2 --large-index -F 10,1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp .simple_tests.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:12 677s @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 1 -x .simple_tests.tmp .simple_tests.gz" 677s 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 677s 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 677s 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 677s Align should not fail when first seq in ref is all Ns (fw:1, sam:1) 677s References: 677s >0 677s NNNNNNNNNNNNNNN 677s >1 677s AGCATCGATCAGTATCTGA 677s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 677s Warning: Encountered reference sequence with only gaps 677s Warning: Encountered reference sequence with only gaps 677s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG 678s @HD VN:1.5 SO:unsorted GO:query 678s @SQ SN:0 LN:15 678s @SQ SN:1 LN:19 678s @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 -c CATCGATCAGTATCTG" 678s 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 678s Align should not fail when multiple seqs are all Ns (fw:1, sam:1) 678s References: 678s >0 678s NNNNNNNNNNNNNNN 678s >1 678s NNNNNNNNNNNNNNN 678s >2 678s AGCATCGATCAGTATCTGA 678s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 678s Warning: Encountered reference sequence with only gaps 678s Warning: Encountered reference sequence with only gaps 678s Warning: Encountered reference sequence with only gaps 678s Warning: Encountered reference sequence with only gaps 679s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:15 679s @SQ SN:1 LN:15 679s @SQ SN:2 LN:19 679s @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 CATCGATCAGTATCTG" 679s 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 679s Should account for stretch of Ns at beginning (fw:1, sam:1) 679s References: 679s >0 679s NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 680s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:34 680s @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" 680s 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 680s Cline 1 (fw:1, sam:1) 680s References: 680s >0 680s AGCATCGATCAGTATCTGA 680s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 681s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:19 681s @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" 681s 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 681s Cline 2 (fw:1, sam:1) 681s References: 681s >0 681s AGCATCGATCAGTATCTGA 681s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:19 681s @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:IIIIIIIIIIIIIIII" 681s 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 681s Cline 2 (fw:1, sam:1) 681s References: 681s >0 681s AGCATCGATCAGTATCTGA 681s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:19 682s @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 -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" 682s 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 682s Cline 4 (fw:1, sam:1) 682s References: 682s >0 682s AGCATCGATCAGTATCTGA 682s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO 682s Error: Read 0 has more read characters than quality values. 682s terminate called after throwing an instance of 'int' 683s Aborted (core dumped) 683s (ERR): bowtie2-align exited with value 134 683s Cline 5 (fw:1, sam:1) 683s References: 683s >0 683s AGCATCGATCAGTATCTGA 683s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ 683s Error: Read 0 has more quality values than read characters. 683s terminate called after throwing an instance of 'int' 684s Aborted (core dumped) 684s (ERR): bowtie2-align exited with value 134 684s trim-to: trim from 5'-end (fw:1, sam:1) 684s References: 684s >0 684s AGCATCGATCAGTATCTGA 684s /usr/bin/bowtie2 --large-index --trim-to 5:12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 684s 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:19 684s @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 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 684s 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 684s trim-to: trim from 3'-end (fw:1, sam:1) 684s References: 684s >0 684s AGCATCGATCAGTATCTGA 684s /usr/bin/bowtie2 --large-index --trim-to 3:12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 684s 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:19 684s @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 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 684s 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 684s trim-to: trim from 3'-end (default) (fw:1, sam:1) 684s References: 684s >0 684s AGCATCGATCAGTATCTGA 684s /usr/bin/bowtie2 --large-index --trim-to 12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 684s 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:19 684s @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 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 684s 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 684s trim-to: invalid position (fw:1, sam:1) 684s References: 684s >0 684s AGCATCGATCAGTATCTGA 684s /usr/bin/bowtie2 --large-index --trim-to 4:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 684s 685s --trim-to: trim position must be either 3 or 5 685s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 685s Usage: 685s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 685s 685s Index filename prefix (minus trailing .X.bt2l). 685s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 685s Files with #1 mates, paired with files in . 685s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 685s Files with #2 mates, paired with files in . 685s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 685s Files with unpaired reads. 685s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 685s Files with interleaved paired-end FASTQ/FASTA reads 685s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 685s Files are unaligned BAM sorted by read name. 685s File for SAM output (default: stdout) 685s 685s , , can be comma-separated lists (no whitespace) and can be 685s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 685s 685s Options (defaults in parentheses): 685s 685s Input: 685s -q query input files are FASTQ .fq/.fastq (default) 685s --tab5 query input files are TAB5 .tab5 685s --tab6 query input files are TAB6 .tab6 685s --qseq query input files are in Illumina's qseq format 685s -f query input files are (multi-)FASTA .fa/.mfa 685s -r query input files are raw one-sequence-per-line 685s -F k:,i: query input files are continuous FASTA where reads 685s are substrings (k-mers) extracted from a FASTA file 685s and aligned at offsets 1, 1+i, 1+2i ... end of reference 685s -c , , are sequences themselves, not files 685s -s/--skip skip the first reads/pairs in the input (none) 685s -u/--upto stop after first reads/pairs (no limit) 685s -5/--trim5 trim bases from 5'/left end of reads (0) 685s -3/--trim3 trim bases from 3'/right end of reads (0) 685s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 685s If the read end is not specified then it defaults to 3 (0) 685s --phred33 qualities are Phred+33 (default) 685s --phred64 qualities are Phred+64 685s --int-quals qualities encoded as space-delimited integers 685s 685s Presets: Same as: 685s For --end-to-end: 685s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 685s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 685s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 685s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 685s 685s For --local: 685s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 685s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 685s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 685s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 685s 685s Alignment: 685s -N max # mismatches in seed alignment; can be 0 or 1 (0) 685s -L length of seed substrings; must be >3, <32 (22) 685s -i interval between seed substrings w/r/t read len (S,1,1.15) 685s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 685s --dpad include extra ref chars on sides of DP table (15) 685s --gbar disallow gaps within nucs of read extremes (4) 685s --ignore-quals treat all quality values as 30 on Phred scale (off) 685s --nofw do not align forward (original) version of read (off) 685s --norc do not align reverse-complement version of read (off) 685s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 685s scan for the optimal seeded alignments 685s --end-to-end entire read must align; no clipping (on) 685s OR 685s --local local alignment; ends might be soft clipped (off) 685s 685s Scoring: 685s --ma match bonus (0 for --end-to-end, 2 for --local) 685s --mp max penalty for mismatch; lower qual = lower penalty (6) 685s --np penalty for non-A/C/G/Ts in read/ref (1) 685s --rdg , read gap open, extend penalties (5,3) 685s --rfg , reference gap open, extend penalties (5,3) 685s --score-min min acceptable alignment score w/r/t read length 685s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 685s 685s Reporting: 685s (default) look for multiple alignments, report best, with MAPQ 685s OR 685s -k report up to alns per read; MAPQ not meaningful 685s OR 685s -a/--all report all alignments; very slow, MAPQ not meaningful 685s 685s Effort: 685s -D give up extending after failed extends in a row (15) 685s -R for reads w/ repetitive seeds, try sets of seeds (2) 685s 685s Paired-end: 685s -I/--minins minimum fragment length (0) 685s -X/--maxins maximum fragment length (500) 685s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 685s --no-mixed suppress unpaired alignments for paired reads 685s --no-discordant suppress discordant alignments for paired reads 685s --dovetail concordant when mates extend past each other 685s --no-contain not concordant when one mate alignment contains other 685s --no-overlap not concordant when mates overlap at all 685s 685s BAM: 685s --align-paired-reads 685s Bowtie2 will, by default, attempt to align unpaired BAM reads. 685s Use this option to align paired-end reads instead. 685s --preserve-tags Preserve tags from the original BAM record by 685s appending them to the end of the corresponding SAM output. 685s 685s Output: 685s -t/--time print wall-clock time taken by search phases 685s --un write unpaired reads that didn't align to 685s --al write unpaired reads that aligned at least once to 685s --un-conc write pairs that didn't align concordantly to 685s --al-conc write pairs that aligned concordantly at least once to 685s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 685s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 685s --quiet print nothing to stderr except serious errors 685s --met-file send metrics to file at (off) 685s --met-stderr send metrics to stderr (off) 685s --met report internal counters & metrics every secs (1)trim-to: invalid count (fw:1, sam:1) 685s References: 685s >0 685s AGCATCGATCAGTATCTGA 685s /usr/bin/bowtie2 --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 685s 685s 685s --no-unal suppress SAM records for unaligned reads 685s --no-head suppress header lines, i.e. lines starting with @ 685s --no-sq suppress @SQ header lines 685s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 685s --rg add ("lab:value") to @RG line of SAM header. 685s Note: @RG line only printed when --rg-id is set. 685s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 685s --sam-no-qname-trunc 685s Suppress standard behavior of truncating readname at first whitespace 685s at the expense of generating non-standard SAM. 685s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 685s --soft-clipped-unmapped-tlen 685s Exclude soft-clipped bases when reporting TLEN 685s --sam-append-comment 685s Append FASTA/FASTQ comment to SAM record 685s 685s Performance: 685s -p/--threads number of alignment threads to launch (1) 685s --reorder force SAM output order to match order of input reads 685s --mm use memory-mapped I/O for index; many 'bowtie's can share 685s 685s Other: 685s --qc-filter filter out reads that are bad according to QSEQ filter 685s --seed seed for random number generator (0) 685s --non-deterministic 685s seed rand. gen. arbitrarily instead of using read attributes 685s --version print version information and quit 685s -h/--help print this usage message 685s Error: Encountered internal Bowtie 2 exception (#1) 685s Command: /usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 685s (ERR): bowtie2-align exited with value 1 685s --trim-to: the number bases to trim must be at least 0 685s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 685s Usage: 685s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 685s 685s Index filename prefix (minus trailing .X.bt2l). 685s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 685s Files with #1 mates, paired with files in . 685s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 685s Files with #2 mates, paired with files in . 685s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 685s Files with unpaired reads. 685s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 685s Files with interleaved paired-end FASTQ/FASTA reads 685s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 685s Files are unaligned BAM sorted by read name. 685s File for SAM output (default: stdout) 685s 685s , , can be comma-separated lists (no whitespace) and can be 685s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 685s 685s Options (defaults in parentheses): 685s 685s Input: 685s -q query input files are FASTQ .fq/.fastq (default) 685s --tab5 query input files are TAB5 .tab5 685s --tab6 query input files are TAB6 .tab6 685s --qseq query input files are in Illumina's qseq format 685s -f query input files are (multi-)FASTA .fa/.mfa 685s -r query input files are raw one-sequence-per-line 685s -F k:,i: query input files are continuous FASTA where reads 685s are substrings (k-mers) extracted from a FASTA file 685s and aligned at offsets 1, 1+i, 1+2i ... end of reference 685s -c , , are sequences themselves, not files 685s -s/--skip skip the first reads/pairs in the input (none) 685s -u/--upto stop after first reads/pairs (no limit) 685s -5/--trim5 trim bases from 5'/left end of reads (0) 685s -3/--trim3 trim bases from 3'/right end of reads (0) 685s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 685s If the read end is not specified then it defaults to 3 (0) 685s --phred33 qualities are Phred+33 (default) 685s --phred64 qualities are Phred+64 685s --int-quals qualities encoded as space-delimited integers 685s 685s Presets: Same as: 685s For --end-to-end: 685s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 685s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 685s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 685s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 685s 685s For --local: 685s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 685s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 685s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 685s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 685s 685s Alignment: 685s -N max # mismatches in seed alignment; can be 0 or 1 (0) 685s -L length of seed substrings; must be >3, <32 (22) 685s -i interval between seed substrings w/r/t read len (S,1,1.15) 685s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 685s --dpad include extra ref chars on sides of DP table (15) 685s --gbar disallow gaps within nucs of read extremes (4) 685s --ignore-quals treat all quality values as 30 on Phred scale (off) 685s --nofw do not align forward (original) version of read (off) 685s --norc do not align reverse-complement version of read (off) 685s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 685s scan for the optimal seeded alignments 685s --end-to-end entire read must align; no clipping (on) 685s OR 685s --local local alignment; ends might be soft clipped (off) 685s 685s Scoring: 685s --ma match bonus (0 for --end-to-end, 2 for --local) 685s --mp max penalty for mismatch; lower qual = lower penalty (6) 685s --np penalty for non-A/C/G/Ts in read/ref (1) 685s --rdg , read gap open, extend penalties (5,3) 685s --rfg , reference gap open, extend penalties (5,3) 685s --score-min min acceptable alignment score w/r/t read length 685s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 685s 685s Reporting: 685s (default) look for multiple alignments, report best, with MAPQ 685s OR 685s -k report up to alns per read; MAPQ not meaningful 685s OR 685s -a/--all report all alignments; very slow, MAPQ not meaningful 685s 685s Effort: 685s -D give up extending after failed extends in a row (15) 685s -R for reads w/ repetitive seeds, try sets of seeds (2) 685s 685s Paired-end: 685s -I/--minins minimum fragment length (0) 685s -X/--maxins maximum fragment length (500) 685s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 685s --no-mixed suppress unpaired alignments for paired reads 685s --no-discordant suppress discordant alignments for paired reads 685s --dovetail concordant when mates extend past each other 685s --no-contain not concordant when one mate alignment contains other 685s --no-overlap not concordant when mates overlap at all 685s 685s BAM: 685s --align-paired-reads 685s Bowtie2 will, by default, attempt to align unpaired BAM reads. 685s Use this option to align paired-end reads instead. 685s --preserve-tags Preserve tags from the original BAM record by 685s appending them to the end of the corresponding SAM output. 685s 685s Output: 685s -t/--time print wall-clock time taken by search phases 685s --un write unpaired reads that didn't align to 685s --al write unpaired reads that aligned at least once to 685s --un-conc write pairs that didn't align concordantly to 685s --al-conc write pairs that aligned concordantly at least once to 685s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 685s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 685s --quiet print nothing to stderr except serious errors 685s --met-file send metrics to file at (off) 685s --met-stderr send metrics to stderr (off) 685s --met report internal counters & metrics every secs (1) 685s --no-unal suppress SAM records for unaligned reads 685s --no-head suppress header lines, i.e. lines starting with @ 685s --no-sq suppress @SQ header lines 685s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 685s --rg add ("lab:value") to @RG line of SAM header. 685s Note: @RG line only printed when --rg-id is set. 685s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 685s --sam-no-qname-trunc 685s Suppress standard behavior of truncating readname at first whitespace 685s at the expense of generating non-standard SAM. 685s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 685s --soft-clipped-unmapped-tlen 685s Exclude soft-clipped bases when reporting TLEN 685s --sam-append-comment 685s Append FASTA/FASTQ comment to SAM record 685s 685s Performance: 685s -p/--threads number of alignment threads to launch (1) 685s --reorder force SAM output order to match order of input reads 685s --mm use memory-mapped I/O for index; many 'bowtie's can share 685s 685s Other: 685s --qc-filter filter out reads that are bad according to QSEQ filter 685s --seed seed for random number generator (0) 685s --non-deterministic 685s seed rand. gen. arbitrarily instead of using read attributes 685s --version print version information and quit 685s -h/--help print this usage message 685s Error: Encountered internal Bowtie 2 exception (#1) 685s Command: /usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 685s (ERR): bowtie2-align exited with value 1 685s Cline 7 (fw:1, sam:1) 685s References: 685s >0 685s AGCATCGATCAGTATCTGA 685s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 685s 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:19 685s @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 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 685s 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 685s Cline 8 (fw:1, sam:1) 685s References: 685s >0 685s AGCATCGATCAGTATCTGA 685s /usr/bin/bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:19 685s @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 -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 685s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 685s Cline 9 (fw:1, sam:1) 685s References: 685s >0 685s AGCATCGATCAGTATCTGA 685s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:19 686s @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 -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 686s Cline multiread 1 (fw:1, sam:1) 686s References: 686s >0 686s AGCATCGATCAGTATCTGA 686s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 686s 686s 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:19 686s @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 CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 686s 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 686s 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 686s Cline multiread 2 (fw:1, sam:1) 686s References: 686s >0 686s AGCATCGATCAGTATCTGA 686s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 686s 686s 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:19 686s @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" 686s 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 686s Cline multiread 3 (fw:1, sam:1) 686s References: 686s >0 686s AGCATCGATCAGTATCTGA 686s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG 686s 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:19 686s @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 -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" 686s 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 686s 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 687s Cline paired 1 (fw:1, sam:1) 687s References: 687s >0 687s AGCATCGATCAAAAACTGA 687s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 687s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:19 688s @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 -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" 688s 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 688s 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 688s 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 688s 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 688s Cline paired 2 (fw:1, sam:1) 688s References: 688s >0 688s AGCATCGATCAAAAACTGA 688s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:19 688s @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 -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 688s 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 688s 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 688s Cline paired 3 (fw:1, sam:1) 688s References: 688s >0 688s AGCATCGATCAAAAACTGA 688s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:19 688s @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 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 688s 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 688s 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 688s Cline paired 4 (fw:1, sam:1) 688s References: 688s >0 688s AGCATCGATCAAAAACTGA 688s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII 689s @HD VN:1.5 SO:unsorted GO:query 689s @SQ SN:0 LN:19 689s @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 10 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" 689s 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 689s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 689s Fastq 1 (fw:1, sam:1) 689s References: 689s >0 689s AGCATCGATCAGTATCTGA 689s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 689s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:19 690s @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 -q .simple_tests.fq.gz" 690s 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 690s Fastq 2 (fw:1, sam:1) 690s References: 690s >0 690s AGCATCGATCAGTATCTGA 690s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:19 690s @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.fq.gz" 690s 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 690s Fastq 3 (fw:1, sam:1) 690s References: 690s >0 690s AGCATCGATCAGTATCTGA 690s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:19 690s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz" 690s 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 690s Fastq 4 (fw:1, sam:1) 690s References: 690s >0 690s AGCATCGATCAGTATCTGA 690s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz 690s Error: Read r0 has more read characters than quality values. 690s terminate called after throwing an instance of 'int' 691s Aborted (core dumped) 691s (ERR): bowtie2-align exited with value 134 691s Fastq 5 (fw:1, sam:1) 691s References: 691s >0 691s AGCATCGATCAGTATCTGA 691s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz 691s Error: Read r0 has more read characters than quality values. 691s terminate called after throwing an instance of 'int' 692s Aborted (core dumped) 692s (ERR): bowtie2-align exited with value 134 692s Fastq 6 (fw:1, sam:1) 692s References: 692s >0 692s AGCATCGATCAGTATCTGA 692s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz 692s Error: reads file does not look like a FASTQ file 692s terminate called after throwing an instance of 'int' 692s Aborted (core dumped) 692s (ERR): bowtie2-align exited with value 134 692s Fastq 7 (fw:1, sam:1) 692s References: 692s >0 692s AGCATCGATCAGTATCTGA 692s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:19 693s @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 -q .simple_tests.fq.gz" 693s 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 693s Fastq 8 (fw:1, sam:1) 693s References: 693s >0 693s AGCATCGATCAGTATCTGA 693s /usr/bin/bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:19 693s @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 4 -x .simple_tests.tmp -q .simple_tests.fq.gz" 693s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 693s Fastq 9 (fw:1, sam:1) 693s References: 693s >0 693s AGCATCGATCAGTATCTGA 693s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:19 693s @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 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" 693s Fastq multiread 1 (fw:1, sam:1) 693s References: 693s >0 693s AGCATCGATCAGTATCTGA 693s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:19 693s @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 -q .simple_tests.fq.gz" 693s 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 693s 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 693s Fastq multiread 2 (fw:1, sam:1) 693s References: 693s >0 693s AGCATCGATCAGTATCTGA 693s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz 694s @HD VN:1.5 SO:unsorted GO:query 694s @SQ SN:0 LN:19 694s @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 -q .simple_tests.fq.gz" 694s 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 694s Fastq multiread 3 (fw:1, sam:1) 694s References: 694s >0 694s AGCATCGATCAGTATCTGA 694s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz 694s @HD VN:1.5 SO:unsorted GO:query 694s @SQ SN:0 LN:19 694s @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 -q .simple_tests.fq.gz" 694s 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 694s 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 694s Fastq paired 1 (fw:1, sam:1) 694s References: 694s >0 694s AGCATCGATCAAAAACTGA 694s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 695s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:19 695s @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 -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 695s 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 695s 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 695s 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 695s 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 695s Fastq paired 2 (fw:1, sam:1) 695s References: 695s >0 695s AGCATCGATCAAAAACTGA 695s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 696s @HD VN:1.5 SO:unsorted GO:query 696s @SQ SN:0 LN:19 696s @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 -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 696s 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 696s 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 696s Fastq paired 3 (fw:1, sam:1) 696s References: 696s >0 696s AGCATCGATCAAAAACTGA 696s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 696s @HD VN:1.5 SO:unsorted GO:query 696s @SQ SN:0 LN:19 696s @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 -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 696s 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 696s 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 696s Fastq paired 4 (fw:1, sam:1) 696s References: 696s >0 696s AGCATCGATCAAAAACTGA 696s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 696s @HD VN:1.5 SO:unsorted GO:query 696s @SQ SN:0 LN:19 696s @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 9 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 696s 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 696s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 696s Fasta 1 (fw:1, sam:1) 696s References: 696s >0 696s AGCATCGATCAGTATCTGA 696s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 697s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz 697s @HD VN:1.5 SO:unsorted GO:query 697s @SQ SN:0 LN:19 697s @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 -f .simple_tests.fa.gz" 697s 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 697s Fasta 2 (fw:1, sam:1) 697s References: 697s >0 697s AGCATCGATCAGTATCTGA 697s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz 697s @HD VN:1.5 SO:unsorted GO:query 697s @SQ SN:0 LN:19 697s @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" 697s 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 697s Fasta 3 (fw:1, sam:1) 697s References: 697s >0 697s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz" 698s 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 698s Fasta 5 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz 698s Error: reads file does not look like a FASTA file 698s terminate called after throwing an instance of 'int' 698s Aborted (core dumped) 698s (ERR): bowtie2-align exited with value 134 698s Fasta 6 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz 699s Error: reads file does not look like a FASTA file 699s terminate called after throwing an instance of 'int' 699s Aborted (core dumped) 699s (ERR): bowtie2-align exited with value 134 699s Fasta 7 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz 699s @HD VN:1.5 SO:unsorted GO:query 699s @SQ SN:0 LN:19 699s @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 -f .simple_tests.fa.gz" 699s 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 699s Fasta 8 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @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 11 -x .simple_tests.tmp -f .simple_tests.fa.gz" 700s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 700s Fasta 9 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAGTATCTGA 700s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @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 .simple_tests.fa.gz" 700s Fasta multiread 1 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAGTATCTGA 700s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @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 -f .simple_tests.fa.gz" 700s 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 700s 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 700s Fasta multiread 2 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAGTATCTGA 700s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @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 -f .simple_tests.fa.gz" 700s 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 700s Fasta multiread 3 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAGTATCTGA 700s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @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" 701s 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 701s 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 701s Fasta multiline 1 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @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 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" 701s 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 701s 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 701s Fasta multiline 2 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @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 -f .simple_tests.fa.gz" 701s 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 701s 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 701s Fasta multiline 3 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @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 -f .simple_tests.fa.gz" 702s 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 702s 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 702s Fasta paired 1 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAAAAACTGA 702s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 703s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 703s @HD VN:1.5 SO:unsorted GO:query 703s @SQ SN:0 LN:19 703s @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 -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 703s 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 703s 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 703s 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 703s 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 703s Fasta paired 2 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAAAAACTGA 703s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 703s @HD VN:1.5 SO:unsorted GO:query 703s @SQ SN:0 LN:19 703s @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 -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 703s 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 703s 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 703s Fasta paired 3 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAAAAACTGA 703s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 703s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @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 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 704s 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 704s 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 704s Fasta paired 4 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAAAAACTGA 704s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @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 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 704s 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 704s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 704s Raw 1 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAGTATCTGA 704s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 705s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @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" 705s 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 705s Raw 2 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAGTATCTGA 705s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @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" 705s 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 705s Raw 3 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAGTATCTGA 705s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @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 -r .simple_tests.raw.gz" 705s 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 705s Raw 7 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAGTATCTGA 705s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz 706s @HD VN:1.5 SO:unsorted GO:query 706s @SQ SN:0 LN:19 706s @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 15 -x .simple_tests.tmp -r .simple_tests.raw.gz" 706s 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 706s Raw 8 (fw:1, sam:1) 706s References: 706s >0 706s AGCATCGATCAGTATCTGA 706s /usr/bin/bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz 706s @HD VN:1.5 SO:unsorted GO:query 706s @SQ SN:0 LN:19 706s @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 9 -x .simple_tests.tmp -r .simple_tests.raw.gz" 706s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 706s Raw 9 (fw:1, sam:1) 706s References: 706s >0 706s AGCATCGATCAGTATCTGA 706s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz 706s @HD VN:1.5 SO:unsorted GO:query 706s @SQ SN:0 LN:19 706s @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 -r .simple_tests.raw.gz" 706s Raw multiread 1 (fw:1, sam:1) 706s References: 706s >0 706s AGCATCGATCAGTATCTGA 706s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz 706s @HD VN:1.5 SO:unsorted GO:query 706s @SQ SN:0 LN:19 706s @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" 706s 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 706s 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 706s Raw multiread 2 (fw:1, sam:1) 706s References: 706s >0 706s AGCATCGATCAGTATCTGA 706s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz 707s @HD VN:1.5 SO:unsorted GO:query 707s @SQ SN:0 LN:19 707s @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 5 -x .simple_tests.tmp -r .simple_tests.raw.gz" 707s 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 707s Raw multiread 3 (fw:1, sam:1) 707s References: 707s >0 707s AGCATCGATCAGTATCTGA 707s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz 707s @HD VN:1.5 SO:unsorted GO:query 707s @SQ SN:0 LN:19 707s @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 -r .simple_tests.raw.gz" 707s 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 707s 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 707s Raw paired 1 (fw:1, sam:1) 707s References: 707s >0 707s AGCATCGATCAAAAACTGA 707s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 708s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 708s @HD VN:1.5 SO:unsorted GO:query 708s @SQ SN:0 LN:19 708s @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 -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 708s 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 708s 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 708s 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 708s 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 708s Raw paired 2 (fw:1, sam:1) 708s References: 708s >0 708s AGCATCGATCAAAAACTGA 708s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 708s @HD VN:1.5 SO:unsorted GO:query 708s @SQ SN:0 LN:19 708s @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 4 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 708s 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 708s 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 708s Raw paired 3 (fw:1, sam:1) 708s References: 708s >0 708s AGCATCGATCAAAAACTGA 708s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:19 709s @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 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 709s 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 709s 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 709s Raw paired 4 (fw:1, sam:1) 709s References: 709s >0 709s AGCATCGATCAAAAACTGA 709s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:19 709s @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 13 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 709s 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 709s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 709s Tabbed 1 (fw:1, sam:1) 709s References: 709s >0 709s AGCATCGATCAGTATCTGA 709s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 710s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:19 710s @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 --tab5 .simple_tests.tab.gz" 710s 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 710s Tabbed 2 (fw:1, sam:1) 710s References: 710s >0 710s AGCATCGATCAGTATCTGA 710s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:19 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 710s 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 710s Tabbed 3 (fw:1, sam:1) 710s References: 710s >0 710s AGCATCGATCAGTATCTGA 710s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:19 710s @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" 710s 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 710s Tabbed 4 (fw:1, sam:1) 710s References: 710s >0 710s AGCATCGATCAGTATCTGA 710s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 711s Error: Read r0 has more read characters than quality values. 711s terminate called after throwing an instance of 'int' 711s Aborted (core dumped) 711s (ERR): bowtie2-align exited with value 134 711s Tabbed 5 (fw:1, sam:1) 711s References: 711s >0 711s AGCATCGATCAGTATCTGA 711s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 711s Error: Read r0 has more quality values than read characters. 711s terminate called after throwing an instance of 'int' 712s Aborted (core dumped) 712s (ERR): bowtie2-align exited with value 134 712s Tabbed 7 (fw:1, sam:1) 712s References: 712s >0 712s AGCATCGATCAGTATCTGA 712s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:19 712s @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" 712s 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 712s Tabbed 8 (fw:1, sam:1) 712s References: 712s >0 712s AGCATCGATCAGTATCTGA 712s /usr/bin/bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:19 712s @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 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 712s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 712s Tabbed 9 (fw:1, sam:1) 712s References: 712s >0 712s AGCATCGATCAGTATCTGA 712s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:19 713s @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 --tab5 .simple_tests.tab.gz" 713s Tabbed multiread 1 (fw:1, sam:1) 713s References: 713s >0 713s AGCATCGATCAGTATCTGA 713s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:19 713s @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 --tab5 .simple_tests.tab.gz" 713s 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 713s 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 713s Tabbed multiread 2 (fw:1, sam:1) 713s References: 713s >0 713s AGCATCGATCAGTATCTGA 713s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:19 713s @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 --tab5 .simple_tests.tab.gz" 713s 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 713s Tabbed multiread 3 (fw:1, sam:1) 713s References: 713s >0 713s AGCATCGATCAGTATCTGA 713s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:19 713s @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 --tab5 .simple_tests.tab.gz" 713s 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 713s 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 713s Tabbed paired 1 (fw:1, sam:1) 713s References: 713s >0 713s AGCATCGATCAAAAACTGA 713s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 714s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 714s @HD VN:1.5 SO:unsorted GO:query 714s @SQ SN:0 LN:19 714s @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 --tab5 .simple_tests.tab.gz" 714s 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 714s 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 714s 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 714s 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 714s Tabbed paired 2 (fw:1, sam:1) 714s References: 714s >0 714s AGCATCGATCAAAAACTGA 714s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:19 715s @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 --tab5 .simple_tests.tab.gz" 715s 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 715s 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 715s Tabbed paired 3 (fw:1, sam:1) 715s References: 715s >0 715s AGCATCGATCAAAAACTGA 715s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:19 715s @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 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 715s 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 715s 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 715s Tabbed paired 4 (fw:1, sam:1) 715s References: 715s >0 715s AGCATCGATCAAAAACTGA 715s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:19 715s @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 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 715s 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 715s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 715s Qseq 1 (fw:1, sam:1) 715s References: 715s >0 715s AGCATCGATCAGTATCTGA 715s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 716s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:19 716s @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" 716s 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 716s Qseq 2 Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 716s (fw:1, sam:1) 716s References: 716s >0 716s AGCATCGATCAGTATCTGA 716s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:19 717s @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 --qseq .simple_tests_qseq.txt.gz" 717s 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 717s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 717s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 717s Qseq 3 (fw:1, sam:1) 717s References: 717s >0 717s AGCATCGATCAGTATCTGA 717s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:19 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 717s 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 717s Qseq 4 (fw:1, sam:1) 717s References: 717s >0 717s AGCATCGATCAGTATCTGA 717s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 717s Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values. 717s terminate called after throwing an instance of 'int' 717s Aborted (core dumped) 717s (ERR): bowtie2-align exited with value 134 717s Qseq 7 (fw:1, sam:1) 717s References: 717s >0 717s AGCATCGATCAGTATCTGA 717s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:19 718s @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 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 718s 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 718s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 718s Qseq 8 (fw:1, sam:1) 718s References: 718s >0 718s AGCATCGATCAGTATCTGA 718s /usr/bin/bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:19 718s @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 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 718s MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 718s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 718s Qseq 9 (fw:1, sam:1) 718s References: 718s >0 718s AGCATCGATCAGTATCTGA 718s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:19 718s @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 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 718s Qseq multiread 1 (fw:1, sam:1) 718s References: 718s >0 718s AGCATCGATCAGTATCTGA 718s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:19 718s @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 --qseq .simple_tests_qseq.txt.gz" 718s 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 718s 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 718s Qseq multiread 2 (fw:1, sam:1) 718s References: 718s >0 718s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @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 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 719s 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 719s Qseq multiread 3 (fw:1, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @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 --qseq .simple_tests_qseq.txt.gz" 719s 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 719s 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 719s Qseq paired 1 (fw:1, sam:1) 719s References: 719s >0 719s AGCATCGATCAAAAACTGA 719s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 720s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:19 720s @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 -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 720s 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 720s 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 720s 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 720s 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 720s Qseq paired 2 (fw:1, sam:1) 720s References: 720s >0 720s AGCATCGATCAAAAACTGA 720s /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 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:19 720s @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" 720s 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 720s 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 720s Left-align insertion (fw:1, sam:1) 720s References: 720s >0 720s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 720s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 721s /usr/bin/bowtie2 --large-index --quiet --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:73 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 721s 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 722s Left-align deletion (fw:1, sam:1) 722s References: 722s >0 722s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 722s /usr/bin/bowtie2 --large-index --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:73 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 722s 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 722s Left-align insertion with mismatch at LHS (fw:1, sam:1) 722s References: 722s >0 722s GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 722s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 723s /usr/bin/bowtie2 --large-index --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:73 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 723s 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 723s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 723s References: 723s >0 723s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 723s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 724s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:1192 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 724s 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 724s 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 724s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 724s References: 724s >0 724s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG 724s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 725s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:1028 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 725s 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 725s 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 725s MREVERSE flag is set if mate does not align (fw:1, sam:1) 725s References: 725s >0 725s TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG 725s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 726s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:250 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 726s 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 726s r0 165 0 51 0 * = 51 0 CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 726s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 726s References: 726s >0 726s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 726s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 728s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 728s @HD VN:1.5 SO:unsorted GO:query 728s @SQ SN:0 LN:290 728s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 728s 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 728s 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 728s MD:Z 1 (fw:1, sam:1) 728s References: 728s >0 728s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 728s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 728s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 728s @HD VN:1.5 SO:unsorted GO:query 728s @SQ SN:0 LN:54 728s @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" 728s 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 728s MD:Z 1 (fw:0, sam:1) 728s References: 728s >0 728s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 728s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 729s @HD VN:1.5 SO:unsorted GO:query 729s @SQ SN:0 LN:54 729s @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" 729s 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 729s MD:Z 2 (fw:1, sam:1) 729s References: 729s >0 729s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 729s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 730s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 730s @HD VN:1.5 SO:unsorted GO:query 730s @SQ SN:0 LN:54 730s @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" 730s 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 730s MD:Z 2 (fw:0, sam:1) 730s References: 730s >0 730s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 730s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 730s @HD VN:1.5 SO:unsorted GO:query 730s @SQ SN:0 LN:54 730s @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" 730s 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 730s MD:Z 3 (fw:1, sam:1) 730s References: 730s >0 730s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 730s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 731s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 731s @HD VN:1.5 SO:unsorted GO:query 731s @SQ SN:0 LN:55 731s @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" 731s 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 731s MD:Z 3 (fw:0, sam:1) 731s References: 731s >0 731s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 731s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 732s @HD VN:1.5 SO:unsorted GO:query 732s @SQ SN:0 LN:55 732s @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" 732s 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 732s MD:Z 4 (fw:1, sam:1) 732s References: 732s >0 732s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 732s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 733s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 733s @HD VN:1.5 SO:unsorted GO:query 733s @SQ SN:0 LN:55 733s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 733s 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 733s MD:Z 4 (fw:0, sam:1) 733s References: 733s >0 733s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 733s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 733s @HD VN:1.5 SO:unsorted GO:query 733s @SQ SN:0 LN:55 733s @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 -q .simple_tests.1a.fq.gz" 733s 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 733s Local alignment 1 (fw:1, sam:1) 733s References: 733s >0 733s TTGT 733s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 734s /usr/bin/bowtie2 --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 734s @HD VN:1.5 SO:unsorted GO:query 734s @SQ SN:0 LN:4 734s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 734s 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 734s Local alignment 1 (fw:0, sam:1) 734s References: 734s >0 734s TTGT 734s /usr/bin/bowtie2 --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 735s @HD VN:1.5 SO:unsorted GO:query 735s @SQ SN:0 LN:4 735s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 735s 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 735s Local alignment 2 (fw:1, sam:1) 735s References: 735s >0 735s TTGA 735s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 736s /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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 736s @HD VN:1.5 SO:unsorted GO:query 736s @SQ SN:0 LN:4 736s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 736s 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 736s Local alignment 2 (fw:0, sam:1) 736s References: 736s >0 736s TTGA 736s /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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 736s @HD VN:1.5 SO:unsorted GO:query 736s @SQ SN:0 LN:4 736s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 736s 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 736s Local alignment 3 (fw:1, sam:1) 736s References: 736s >0 736s TTGTTCGTTTGTTCGT 736s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 737s /usr/bin/bowtie2 --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 737s @HD VN:1.5 SO:unsorted GO:query 737s @SQ SN:0 LN:16 737s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 737s 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 737s 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 737s Local alignment 3 (fw:0, sam:1) 737s References: 737s >0 737s TTGTTCGTTTGTTCGT 737s /usr/bin/bowtie2 --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 737s @HD VN:1.5 SO:unsorted GO:query 737s @SQ SN:0 LN:16 737s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 737s 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 737s 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 737s Local alignment 4 (fw:1, sam:1) 737s References: 737s >0 737s TTGTTCGTTTGTTCGT 737s /usr/bin/bowtie2 --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 738s @HD VN:1.5 SO:unsorted GO:query 738s @SQ SN:0 LN:16 738s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 738s 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 738s 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 738s Local alignment 4 (fw:0, sam:1) 738s References: 738s >0 738s TTGTTCGTTTGTTCGT 738s /usr/bin/bowtie2 --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 738s @HD VN:1.5 SO:unsorted GO:query 738s @SQ SN:0 LN:16 738s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 738s 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 738s 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 738s Alignment order -k (fw:1, sam:1) 738s References: 738s >0 738s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 738s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 739s /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 739s @HD VN:1.5 SO:unsorted GO:query 739s @SQ SN:0 LN:86 739s @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" 739s 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 739s 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 739s 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 739s 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 739s Alignment order -k (fw:0, sam:1) 739s References: 739s >0 739s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 739s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 739s @HD VN:1.5 SO:unsorted GO:query 739s @SQ SN:0 LN:86 739s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 739s 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 739s 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 739s 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 739s 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 739s Alignment order -a (fw:1, sam:1) 739s References: 739s >0 739s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 739s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 740s @HD VN:1.5 SO:unsorted GO:query 740s @SQ SN:0 LN:86 740s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 740s 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 740s 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 740s 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 740s 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 740s Alignment order -a (fw:0, sam:1) 740s References: 740s >0 740s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 740s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 740s @HD VN:1.5 SO:unsorted GO:query 740s @SQ SN:0 LN:86 740s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 740s 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 740s 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 740s 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 740s 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 740s Mate reporting order, -a (fw:1, sam:1) 740s References: 740s >0 740s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 740s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 741s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 2 -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 741s @HD VN:1.5 SO:unsorted GO:query 741s @SQ SN:0 LN:407 741s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -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" 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s 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 741s Mate reporting order, -a (fw:0, sam:1) 741s References: 741s >0 741s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 741s /usr/bin/bowtie2 --large-index --fr --quiet -a --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 742s @HD VN:1.5 SO:unsorted GO:query 742s @SQ SN:0 LN:407 742s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --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" 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s Mate reporting order, -M 1 (fw:1, sam:1) 742s References: 742s >0 742s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 742s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --reads-per-batch 13 -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 742s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 742s @HD VN:1.5 SO:unsorted GO:query 742s @SQ SN:0 LN:407 742s @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 13 -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" 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s Mate reporting order, -M 1 (fw:0, sam:1) 742s References: 742s >0 742s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 742s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --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 742s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 742s @HD VN:1.5 SO:unsorted GO:query 742s @SQ SN:0 LN:407 742s @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 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" 742s 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 742s 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 742s 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 742s 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 742s 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 742s 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 742s Non-overlapping; no args (fw:1, sam:1) 742s References: 742s >0 742s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 742s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 743s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 743s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s @HD VN:1.5 SO:unsorted GO:query 744s @SQ SN:0 LN:47 744s @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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 744s 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 744s 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 744s Non-overlapping; no args (fw:0, sam:1) 744s References: 744s >0 744s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 744s /usr/bin/bowtie2 --large-index --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 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s @HD VN:1.5 SO:unsorted GO:query 744s @SQ SN:0 LN:47 744s @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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 744s 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 744s 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 744s Non-overlapping; --no-discordant (fw:1, sam:1) 744s References: 744s >0 744s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 744s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s @HD VN:1.5 SO:unsorted GO:query 744s @SQ SN:0 LN:47 744s @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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 744s 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 744s 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 744s Non-overlapping; --no-discordant (fw:0, sam:1) 744s References: 744s >0 744s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 744s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 745s @HD VN:1.5 SO:unsorted GO:query 745s @SQ SN:0 LN:47 745s @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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 745s 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 745s 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 745s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 745s References: 745s >0 745s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 745s /usr/bin/bowtie2 --large-index --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 745s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 745s @HD VN:1.5 SO:unsorted GO:query 745s @SQ SN:0 LN:47 745s @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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 745s 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 745s 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 745s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 745s References: 745s >0 745s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 745s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 745s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 745s @HD VN:1.5 SO:unsorted GO:query 745s @SQ SN:0 LN:47 745s @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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 745s 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 745s 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 745s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 745s References: 745s >0 745s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 745s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 745s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 745s @HD VN:1.5 SO:unsorted GO:query 745s @SQ SN:0 LN:47 745s @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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 745s 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 745s 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 745s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 745s References: 745s >0 745s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 745s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 746s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 746s @HD VN:1.5 SO:unsorted GO:query 746s @SQ SN:0 LN:47 746s @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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 746s 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 746s 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 746s Non-overlapping; --no-dovetail (fw:1, sam:1) 746s References: 746s >0 746s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 746s /usr/bin/bowtie2 --large-index --no-dovetail --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 746s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 746s @HD VN:1.5 SO:unsorted GO:query 746s @SQ SN:0 LN:47 746s @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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 746s 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 746s 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 746s Non-overlapping; --no-dovetail (fw:0, sam:1) 746s References: 746s >0 746s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 746s /usr/bin/bowtie2 --large-index --no-dovetail --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 746s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 746s @HD VN:1.5 SO:unsorted GO:query 746s @SQ SN:0 LN:47 746s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 746s 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 746s 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 746s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1) 746s References: 746s >0 746s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 746s /usr/bin/bowtie2 --large-index --un-conc=.tmp.simple_tests.pl --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 747s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 747s @HD VN:1.5 SO:unsorted GO:query 747s @SQ SN:0 LN:47 747s @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 16 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 747s 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 747s 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 747s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1) 747s References: 747s >0 747s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 747s /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 747s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 747s @HD VN:1.5 SO:unsorted GO:query 747s @SQ SN:0 LN:47 747s @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" 747s 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 747s 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 747s Non-overlapping; --no-overlap (fw:1, sam:1) 747s References: 747s >0 747s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 747s /usr/bin/bowtie2 --large-index --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 747s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 747s @HD VN:1.5 SO:unsorted GO:query 747s @SQ SN:0 LN:47 747s @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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 747s 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 747s 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 747s Non-overlapping; --no-overlap (fw:0, sam:1) 747s References: 747s >0 747s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 747s /usr/bin/bowtie2 --large-index --no-overlap --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 747s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 747s @HD VN:1.5 SO:unsorted GO:query 747s @SQ SN:0 LN:47 747s @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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 747s 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 747s 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 747s Overlapping; no args (fw:1, sam:1) 747s References: 747s >0 747s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 747s /usr/bin/bowtie2 --large-index --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 748s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 748s @HD VN:1.5 SO:unsorted GO:query 748s @SQ SN:0 LN:47 748s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 748s 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 748s 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 748s Overlapping; no args (fw:0, sam:1) 748s References: 748s >0 748s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 748s /usr/bin/bowtie2 --large-index --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 748s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 748s @HD VN:1.5 SO:unsorted GO:query 748s @SQ SN:0 LN:47 748s @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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 748s 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 748s 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 748s Overlapping; --no-dovetail (fw:1, sam:1) 748s References: 748s >0 748s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 748s /usr/bin/bowtie2 --large-index --no-dovetail --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 748s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 748s @HD VN:1.5 SO:unsorted GO:query 748s @SQ SN:0 LN:47 748s @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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 748s 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 748s 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 748s Overlapping; --no-dovetail (fw:0, sam:1) 748s References: 748s >0 748s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 748s /usr/bin/bowtie2 --large-index --no-dovetail --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 748s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 749s @HD VN:1.5 SO:unsorted GO:query 749s @SQ SN:0 LN:47 749s @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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 749s 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 749s 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 749s Overlapping; --no-contain (fw:1, sam:1) 749s References: 749s >0 749s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 749s /usr/bin/bowtie2 --large-index --no-contain --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 749s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 749s @HD VN:1.5 SO:unsorted GO:query 749s @SQ SN:0 LN:47 749s @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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 749s 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 749s 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 749s Overlapping; --no-contain (fw:0, sam:1) 749s References: 749s >0 749s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 749s /usr/bin/bowtie2 --large-index --no-contain --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 749s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 749s @HD VN:1.5 SO:unsorted GO:query 749s @SQ SN:0 LN:47 749s @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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 749s 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 749s 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 749s Overlapping; --no-overlap (fw:1, sam:1) 749s References: 749s >0 749s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 749s /usr/bin/bowtie2 --large-index --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 749s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 749s @HD VN:1.5 SO:unsorted GO:query 749s @SQ SN:0 LN:47 749s @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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 749s 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 749s 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 749s Overlapping; --no-overlap (fw:0, sam:1) 749s References: 749s >0 749s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 749s /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 750s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 750s @HD VN:1.5 SO:unsorted GO:query 750s @SQ SN:0 LN:47 750s @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" 750s 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 750s 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 750s Scoring params 1 (fw:1, sam:1) 750s References: 750s >0 750s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 750s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 751s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 751s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 751s @HD VN:1.5 SO:unsorted GO:query 751s @SQ SN:0 LN:105 751s @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" 751s 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 751s Scoring params 1 (fw:0, sam:1) 751s References: 751s >0 751s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 751s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 751s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 751s @HD VN:1.5 SO:unsorted GO:query 751s @SQ SN:0 LN:105 751s @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" 751s 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 751s Scoring params 2 (fw:1, sam:1) 751s References: 751s >0 751s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 751s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 752s /usr/bin/bowtie2 --large-index --ignore-quals --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 752s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 752s @HD VN:1.5 SO:unsorted GO:query 752s @SQ SN:0 LN:102 752s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 752s 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 752s Scoring params 2 (fw:0, sam:1) 752s References: 752s >0 752s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 752s /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 752s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 752s @HD VN:1.5 SO:unsorted GO:query 752s @SQ SN:0 LN:102 752s @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" 752s 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 752s Scoring params 3 (fw:1, sam:1) 752s References: 752s >0 752s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 752s /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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 753s @HD VN:1.5 SO:unsorted GO:query 753s @SQ SN:0 LN:102 753s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 753s 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 753s Scoring params 3 (fw:0, sam:1) 753s References: 753s >0 753s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 753s /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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 753s @HD VN:1.5 SO:unsorted GO:query 753s @SQ SN:0 LN:102 753s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 753s 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 753s Scoring params 4 (fw:1, sam:1) 753s References: 753s >0 753s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 753s /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 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 753s @HD VN:1.5 SO:unsorted GO:query 753s @SQ SN:0 LN:102 753s @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" 753s 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 753s Scoring params 4 (fw:0, sam:1) 753s References: 753s >0 753s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 753s /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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 754s @HD VN:1.5 SO:unsorted GO:query 754s @SQ SN:0 LN:102 754s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 754s 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 754s Scoring params 5 (fw:1, sam:1) 754s References: 754s >0 754s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 754s /usr/bin/bowtie2 --large-index --ignore-quals --mp 8 --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 754s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 754s @HD VN:1.5 SO:unsorted GO:query 754s @SQ SN:0 LN:102 754s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 754s 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 754s Scoring params 5 (fw:0, sam:1) 754s References: 754s >0 754s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 754s /usr/bin/bowtie2 --large-index --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 754s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 754s @HD VN:1.5 SO:unsorted GO:query 754s @SQ SN:0 LN:102 754s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 754s 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 754s Scoring params 6 (fw:1, sam:1) 754s References: 754s >0 754s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 754s /usr/bin/bowtie2 --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 754s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 754s @HD VN:1.5 SO:unsorted GO:query 754s @SQ SN:0 LN:102 754s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 754s 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 754s Scoring params 6 (fw:0, sam:1) 754s References: 754s >0 754s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 754s /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 755s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 755s @HD VN:1.5 SO:unsorted GO:query 755s @SQ SN:0 LN:102 755s @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" 755s 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 755s Q XS:i 1a (fw:1, sam:1) 755s References: 755s >0 755s TTGTTCGATTGTTCGA 755s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 756s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 756s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 756s @HD VN:1.5 SO:unsorted GO:query 756s @SQ SN:0 LN:16 756s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 756s 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 756s Q XS:i 1a (fw:0, sam:1) 756s References: 756s >0 756s TTGTTCGATTGTTCGA 756s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 756s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 756s @HD VN:1.5 SO:unsorted GO:query 756s @SQ SN:0 LN:16 756s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 756s 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 756s Q XS:i 1a ! --mp 3,3 (fw:1, sam:1) 756s References: 756s >0 756s TTGTTCGATTGTTCGA 756s /usr/bin/bowtie2 --large-index -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 756s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 756s @HD VN:1.5 SO:unsorted GO:query 756s @SQ SN:0 LN:16 756s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 756s 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 756s Q XS:i 1a ! --mp 3,3 (fw:0, sam:1) 756s References: 756s >0 756s TTGTTCGATTGTTCGA 756s /usr/bin/bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 757s @HD VN:1.5 SO:unsorted GO:query 757s @SQ SN:0 LN:16 757s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 757s 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 757s Q XS:i 1a ! --mp 3,6 (fw:1, sam:1) 757s References: 757s >0 757s TTGTTCGATTGTTCGA 757s /usr/bin/bowtie2 --large-index -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 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 757s @HD VN:1.5 SO:unsorted GO:query 757s @SQ SN:0 LN:16 757s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 757s 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 757s Q XS:i 1a ! --mp 3,6 (fw:0, sam:1) 757s References: 757s >0 757s TTGTTCGATTGTTCGA 757s /usr/bin/bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 757s @HD VN:1.5 SO:unsorted GO:query 757s @SQ SN:0 LN:16 757s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 757s 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 757s Q XS:i 1a I --mp 3,3 (fw:1, sam:1) 757s References: 757s >0 757s TTGTTCGATTGTTCGA 757s /usr/bin/bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 758s @HD VN:1.5 SO:unsorted GO:query 758s @SQ SN:0 LN:16 758s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 758s 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 758s Q XS:i 1a I --mp 3,3 (fw:0, sam:1) 758s References: 758s >0 758s TTGTTCGATTGTTCGA 758s /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 758s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 758s @HD VN:1.5 SO:unsorted GO:query 758s @SQ SN:0 LN:16 758s @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" 758s 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 758s Q XS:i 1a I --mp 3,6 (fw:1, sam:1) 758s References: 758s >0 758s TTGTTCGATTGTTCGA 758s /usr/bin/bowtie2 --large-index -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 758s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 758s @HD VN:1.5 SO:unsorted GO:query 758s @SQ SN:0 LN:16 758s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 758s 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 758s Q XS:i 1a I --mp 3,6 (fw:0, sam:1) 758s References: 758s >0 758s TTGTTCGATTGTTCGA 758s /usr/bin/bowtie2 --large-index -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 758s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 758s @HD VN:1.5 SO:unsorted GO:query 758s @SQ SN:0 LN:16 758s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 758s 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 758s Q XS:i 1a --ignore-quals (fw:1, sam:1) 758s References: 758s >0 758s TTGTTCGATTGTTCGA 758s /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 759s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 759s @HD VN:1.5 SO:unsorted GO:query 759s @SQ SN:0 LN:16 759s @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" 759s 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 759s Q XS:i 1a --ignore-quals (fw:0, sam:1) 759s References: 759s >0 759s TTGTTCGATTGTTCGA 759s /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 759s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 759s @HD VN:1.5 SO:unsorted GO:query 759s @SQ SN:0 LN:16 759s @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" 759s 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 759s Q XS:i 1b (fw:1, sam:1) 759s References: 759s >0 759s TTGTTCGATTGTTCGA 759s /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 759s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 759s @HD VN:1.5 SO:unsorted GO:query 759s @SQ SN:0 LN:16 759s @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" 759s 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 759s Q XS:i 1b (fw:0, sam:1) 759s References: 759s >0 759s TTGTTCGATTGTTCGA 759s /usr/bin/bowtie2 --large-index --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 759s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 759s @HD VN:1.5 SO:unsorted GO:query 759s @SQ SN:0 LN:16 759s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 759s 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 759s Q XS:i 1b --ignore-quals (fw:1, sam:1) 759s References: 759s >0 759s TTGTTCGATTGTTCGA 759s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 760s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 760s @HD VN:1.5 SO:unsorted GO:query 760s @SQ SN:0 LN:16 760s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 760s 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 760s Q XS:i 1b --ignore-quals (fw:0, sam:1) 760s References: 760s >0 760s TTGTTCGATTGTTCGA 760s /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 760s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 760s @HD VN:1.5 SO:unsorted GO:query 760s @SQ SN:0 LN:16 760s @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" 760s 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 760s Q XS:i 1c (fw:1, sam:1) 760s References: 760s >0 760s TTGTTCGATTGTTCGA 760s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 760s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 760s @HD VN:1.5 SO:unsorted GO:query 760s @SQ SN:0 LN:16 760s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 760s 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 760s Q XS:i 1c (fw:0, sam:1) 760s References: 760s >0 760s TTGTTCGATTGTTCGA 760s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 760s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 761s @HD VN:1.5 SO:unsorted GO:query 761s @SQ SN:0 LN:16 761s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 761s 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 761s Q XS:i 1c --ignore-quals (fw:1, sam:1) 761s References: 761s >0 761s TTGTTCGATTGTTCGA 761s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 761s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 761s @HD VN:1.5 SO:unsorted GO:query 761s @SQ SN:0 LN:16 761s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 761s 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 761s Q XS:i 1c --ignore-quals (fw:0, sam:1) 761s References: 761s >0 761s TTGTTCGATTGTTCGA 761s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 761s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 761s @HD VN:1.5 SO:unsorted GO:query 761s @SQ SN:0 LN:16 761s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 761s 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 761s (fw:1, sam:1) 761s References: 761s >0 761s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 761s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 762s /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 762s @HD VN:1.5 SO:unsorted GO:query 762s @SQ SN:0 LN:68 762s @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" 762s 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 762s r0 133 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 762s (fw:0, sam:1) 762s References: 762s >0 762s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 762s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 762s @HD VN:1.5 SO:unsorted GO:query 762s @SQ SN:0 LN:68 762s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 762s 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 762s r0 69 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 762s (fw:1, sam:1) 762s References: 762s >0 762s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 762s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 763s /usr/bin/bowtie2 --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 763s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 763s @HD VN:1.5 SO:unsorted GO:query 763s @SQ SN:0 LN:528 763s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 763s 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 764s (fw:0, sam:1) 764s References: 764s >0 764s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 764s /usr/bin/bowtie2 --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 764s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 764s @HD VN:1.5 SO:unsorted GO:query 764s @SQ SN:0 LN:528 764s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 764s 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 764s (fw:1, sam:1) 764s References: 764s >0 764s TTGTTCGTTTGTTCGT 764s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 765s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 765s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 765s @HD VN:1.5 SO:unsorted GO:query 765s @SQ SN:0 LN:16 765s @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" 765s 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 765s (fw:0, sam:1) 765s References: 765s >0 765s TTGTTCGTTTGTTCGT 765s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 765s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 765s @HD VN:1.5 SO:unsorted GO:query 765s @SQ SN:0 LN:16 765s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 765s 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 765s (fw:1, sam:1) 765s References: 765s >0 765s TTGTTCGTTTGTTCGT 765s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 765s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 765s @HD VN:1.5 SO:unsorted GO:query 765s @SQ SN:0 LN:16 765s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 765s 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 765s (fw:0, sam:1) 765s References: 765s >0 765s TTGTTCGTTTGTTCGT 765s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 766s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 766s @HD VN:1.5 SO:unsorted GO:query 766s @SQ SN:0 LN:16 766s @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" 766s 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 766s XS:i 1 (fw:1, sam:1) 766s References: 766s >0 766s TTGTTCGATTGTTCGA 766s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 767s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 767s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 767s @HD VN:1.5 SO:unsorted GO:query 767s @SQ SN:0 LN:16 767s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 767s 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 767s XS:i 1 (fw:0, sam:1) 767s References: 767s >0 767s TTGTTCGATTGTTCGA 767s /usr/bin/bowtie2 --large-index --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 767s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 767s @HD VN:1.5 SO:unsorted GO:query 767s @SQ SN:0 LN:16 767s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 767s 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 767s XS:i 2 (fw:1, sam:1) 767s References: 767s >0 767s TTGTTCGATTGTTCGA 767s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 767s @HD VN:1.5 SO:unsorted GO:query 767s @SQ SN:0 LN:16 767s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 767s r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU 767s XS:i 2 (fw:0, sam:1) 767s References: 767s >0 767s TTGTTCGATTGTTCGA 767s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 768s @HD VN:1.5 SO:unsorted GO:query 768s @SQ SN:0 LN:16 768s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 768s r0 4 * 0 0 * * 0 0 ACGAACAA IIIIIIII YT:Z:UU 768s XS:i 3a (fw:1, sam:1) 768s References: 768s >0 768s TTGTTCGATTGTTCGT 768s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 769s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 769s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 769s @HD VN:1.5 SO:unsorted GO:query 769s @SQ SN:0 LN:16 769s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 769s 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 769s XS:i 3a (fw:0, sam:1) 769s References: 769s >0 769s TTGTTCGATTGTTCGT 769s /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 769s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 769s @HD VN:1.5 SO:unsorted GO:query 769s @SQ SN:0 LN:16 769s @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" 769s 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 769s XS:i 3b (fw:1, sam:1) 769s References: 769s >0 769s TTGTTCGATTGTTCGT 769s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 769s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 769s @HD VN:1.5 SO:unsorted GO:query 769s @SQ SN:0 LN:16 769s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 769s 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 769s XS:i 3b (fw:0, sam:1) 769s References: 769s >0 769s TTGTTCGATTGTTCGT 769s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 770s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 770s @HD VN:1.5 SO:unsorted GO:query 770s @SQ SN:0 LN:16 770s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 770s 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 770s XS:i 3c (fw:1, sam:1) 770s References: 770s >0 770s TTGTTCGATTGTTCGT 770s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 770s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 770s @HD VN:1.5 SO:unsorted GO:query 770s @SQ SN:0 LN:16 770s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 770s 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 770s XS:i 3c (fw:0, sam:1) 770s References: 770s >0 770s TTGTTCGATTGTTCGT 770s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 770s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 770s @HD VN:1.5 SO:unsorted GO:query 770s @SQ SN:0 LN:16 770s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 770s 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 770s XS:i 4a (fw:1, sam:1) 770s References: 770s >0 770s TTGTTCAATTGTTCGATTGTTCGT 770s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 771s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 771s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 771s @HD VN:1.5 SO:unsorted GO:query 771s @SQ SN:0 LN:24 771s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 771s 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 771s XS:i 4a (fw:0, sam:1) 771s References: 771s >0 771s TTGTTCAATTGTTCGATTGTTCGT 771s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 772s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 772s @HD VN:1.5 SO:unsorted GO:query 772s @SQ SN:0 LN:24 772s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 772s 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 772s XS:i 4b (fw:1, sam:1) 772s References: 772s >0 772s TTGTTCAATTGTTCGATTGTTCGT 772s /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 772s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 772s @HD VN:1.5 SO:unsorted GO:query 772s @SQ SN:0 LN:24 772s @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" 772s 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 772s XS:i 4b (fw:0, sam:1) 772s References: 772s >0 772s TTGTTCAATTGTTCGATTGTTCGT 772s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 772s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 772s @HD VN:1.5 SO:unsorted GO:query 772s @SQ SN:0 LN:24 772s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 772s 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 772s XS:i 5a (fw:1, sam:1) 772s References: 772s >0 772s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 772s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 773s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 773s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 773s @HD VN:1.5 SO:unsorted GO:query 773s @SQ SN:0 LN:120 773s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 773s 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 773s XS:i 5a (fw:0, sam:1) 773s References: 773s >0 773s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 773s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 773s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 774s @HD VN:1.5 SO:unsorted GO:query 774s @SQ SN:0 LN:120 774s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 774s 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 774s XS:i 5b (fw:1, sam:1) 774s References: 774s >0 774s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 774s /usr/bin/bowtie2 --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 774s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 774s @HD VN:1.5 SO:unsorted GO:query 774s @SQ SN:0 LN:120 774s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 774s 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 774s XS:i 5b (fw:0, sam:1) 774s References: 774s >0 774s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 774s /usr/bin/bowtie2 --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 774s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 774s @HD VN:1.5 SO:unsorted GO:query 774s @SQ SN:0 LN:120 774s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 774s 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 774s BWA-SW-like 1 (fw:1, sam:1) 774s References: 774s >0 774s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 774s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 775s /usr/bin/bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 775s @HD VN:1.5 SO:unsorted GO:query 775s @SQ SN:0 LN:64 775s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 775s 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 775s BWA-SW-like 1 (fw:0, sam:1) 775s References: 775s >0 775s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 775s /usr/bin/bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 775s @HD VN:1.5 SO:unsorted GO:query 775s @SQ SN:0 LN:64 775s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 775s 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 775s BWA-SW-like 2 (fw:1, sam:1) 775s References: 775s >0 775s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 776s /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 776s @HD VN:1.5 SO:unsorted GO:query 776s @SQ SN:0 LN:64 776s @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" 776s 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 776s BWA-SW-like 2 (fw:0, sam:1) 776s References: 776s >0 776s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 776s /usr/bin/bowtie2 --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 776s @HD VN:1.5 SO:unsorted GO:query 776s @SQ SN:0 LN:64 776s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 776s 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 776s BWA-SW-like 3 (fw:1, sam:1) 776s References: 776s >0 776s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 776s /usr/bin/bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 776s @HD VN:1.5 SO:unsorted GO:query 776s @SQ SN:0 LN:64 776s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 776s 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 776s BWA-SW-like 3 (fw:0, sam:1) 776s References: 776s >0 776s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 776s /usr/bin/bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 777s @HD VN:1.5 SO:unsorted GO:query 777s @SQ SN:0 LN:64 777s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 777s 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 777s SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1) 777s References: 777s >0 777s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 777s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 778s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 778s @HD VN:1.5 SO:unsorted GO:query 778s @SQ SN:0 LN:69 778s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 778s 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 778s 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 778s SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1) 778s References: 778s >0 778s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 778s /usr/bin/bowtie2 --large-index --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 778s @HD VN:1.5 SO:unsorted GO:query 778s @SQ SN:0 LN:69 778s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 778s 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 778s 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 778s SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1) 778s References: 778s >0 778s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 778s /usr/bin/bowtie2 --large-index --rf --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 778s @HD VN:1.5 SO:unsorted GO:query 778s @SQ SN:0 LN:69 778s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 778s 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 778s 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 778s SAM paired-end where both mates align 1 (fw:1, sam:1) 778s References: 778s >0 778s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 778s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 779s @HD VN:1.5 SO:unsorted GO:query 779s @SQ SN:0 LN:69 779s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --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" 779s 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 779s 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 779s SAM paired-end where both mates align 2 (fw:1, sam:1) 779s References: 779s >0 779s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 779s /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 779s @HD VN:1.5 SO:unsorted GO:query 779s @SQ SN:0 LN:69 779s @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" 779s 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 779s 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 779s SAM paired-end where both mates align 3 (fw:1, sam:1) 779s References: 779s >0 779s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 779s /usr/bin/bowtie2 --large-index --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 780s @HD VN:1.5 SO:unsorted GO:query 780s @SQ SN:0 LN:69 780s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --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" 780s 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 780s 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 780s SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1) 780s References: 780s >0 780s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 780s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 780s @HD VN:1.5 SO:unsorted GO:query 780s @SQ SN:0 LN:69 780s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 780s 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 780s r0 133 0 4 0 * = 4 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 780s SAM paired-end where neither mate aligns (fw:1, sam:1) 780s References: 780s >0 780s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 780s /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 780s @HD VN:1.5 SO:unsorted GO:query 780s @SQ SN:0 LN:69 780s @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" 780s r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 780s r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 780s SAM paired-end where both mates align, but discordantly (fw:1, sam:1) 780s References: 780s >0 780s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 780s /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 780s @HD VN:1.5 SO:unsorted GO:query 780s @SQ SN:0 LN:69 780s @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" 780s 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 780s 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 780s matchesRef regression 4 (fw:1, sam:1) 780s References: 780s >0 780s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 780s >1 780s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 780s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 781s /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 782s @HD VN:1.5 SO:unsorted GO:query 782s @SQ SN:0 LN:120 782s @SQ SN:1 LN:31 782s @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" 782s r0 4 * 0 0 * * 0 0 ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 782s matchesRef regression 4 (fw:0, sam:1) 782s References: 782s >0 782s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 782s >1 782s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 782s /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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 782s @HD VN:1.5 SO:unsorted GO:query 782s @SQ SN:0 LN:120 782s @SQ SN:1 LN:31 782s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 782s r0 4 * 0 0 * * 0 0 GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 782s matchesRef regression 3 (fw:1, sam:1) 782s References: 782s >0 782s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 782s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 783s /usr/bin/bowtie2 --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 783s @HD VN:1.5 SO:unsorted GO:query 783s @SQ SN:0 LN:53 783s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 783s 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 783s matchesRef regression 3 (fw:0, sam:1) 783s References: 783s >0 783s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 783s /usr/bin/bowtie2 --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 783s @HD VN:1.5 SO:unsorted GO:query 783s @SQ SN:0 LN:53 783s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 783s 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 783s matchesRef regression 2 (fw:1, sam:1) 783s References: 783s >0 783s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 783s >1 783s CCTTGTTNTTAATGCTGCCTGGTTTNG 783s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 784s /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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 784s @HD VN:1.5 SO:unsorted GO:query 784s @SQ SN:0 LN:47 784s @SQ SN:1 LN:27 784s @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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 784s r0 77 * 0 0 * * 0 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 784s r0 141 * 0 0 * * 0 0 ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 784s matchesRef regression 2 (fw:0, sam:1) 784s References: 784s >0 784s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 784s >1 784s CCTTGTTNTTAATGCTGCCTGGTTTNG 784s /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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 785s @HD VN:1.5 SO:unsorted GO:query 785s @SQ SN:0 LN:47 785s @SQ SN:1 LN:27 785s @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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 785s 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 785s 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 785s matchesRef regression 1 (fw:1, sam:1) 785s References: 785s >0 785s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 785s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 786s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 786s @HD VN:1.5 SO:unsorted GO:query 786s @SQ SN:0 LN:61 786s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 786s 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 786s matchesRef regression 1 (fw:0, sam:1) 786s References: 786s >0 786s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 786s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 786s @HD VN:1.5 SO:unsorted GO:query 786s @SQ SN:0 LN:61 786s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 786s 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 786s Discordant with different chromosomes (fw:1, sam:1) 786s References: 786s >0 786s TTTATAAAAATATTTCCCCCCCC 786s >1 786s CCCCCCTGTCGCTACCGCCCCCCCCCCC 786s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 787s /usr/bin/bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 12 -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 787s @HD VN:1.5 SO:unsorted GO:query 787s @SQ SN:0 LN:23 787s @SQ SN:1 LN:28 787s @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 12 -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" 787s 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 787s 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 787s 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 787s 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 787s Discordant with different chromosomes (fw:0, sam:1) 787s References: 787s >0 787s TTTATAAAAATATTTCCCCCCCC 787s >1 787s CCCCCCTGTCGCTACCGCCCCCCCCCCC 787s /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 788s @HD VN:1.5 SO:unsorted GO:query 788s @SQ SN:0 LN:23 788s @SQ SN:1 LN:28 788s @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" 788s 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 788s 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 788s 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 788s 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 788s (fw:1, sam:1) 788s References: 788s >0 788s AGCATCGATCAGTATCTGA 788s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 789s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 789s @HD VN:1.5 SO:unsorted GO:query 789s @SQ SN:0 LN:19 789s @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 -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 789s 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 789s (fw:0, sam:1) 789s References: 789s >0 789s AGCATCGATCAGTATCTGA 789s /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 789s @HD VN:1.5 SO:unsorted GO:query 789s @SQ SN:0 LN:19 789s @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" 789s 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 789s (fw:1, sam:1) 789s References: 789s >0 789s AGCATCGATCAGTATCTGA 789s /usr/bin/bowtie2 --large-index -s 1 --fr --quiet -a --reads-per-batch 12 -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 789s @HD VN:1.5 SO:unsorted GO:query 789s @SQ SN:0 LN:19 789s @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 12 -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" 789s 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 789s 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 789s (fw:0, sam:1) 789s References: 789s >0 789s AGCATCGATCAGTATCTGA 789s /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 790s @HD VN:1.5 SO:unsorted GO:query 790s @SQ SN:0 LN:19 790s @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" 790s 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 790s 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 790s (fw:1, sam:1) 790s References: 790s >0 790s AGCATCGATCAGTATCTGA 790s /usr/bin/bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 790s @HD VN:1.5 SO:unsorted GO:query 790s @SQ SN:0 LN:19 790s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 790s (fw:0, sam:1) 790s References: 790s >0 790s AGCATCGATCAGTATCTGA 790s /usr/bin/bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 790s @HD VN:1.5 SO:unsorted GO:query 790s @SQ SN:0 LN:19 790s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 790s (fw:1, sam:1) 790s References: 790s >0 790s AGCATCGATCAGTATCTGA 790s /usr/bin/bowtie2 --large-index -s 2 --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 791s @HD VN:1.5 SO:unsorted GO:query 791s @SQ SN:0 LN:19 791s @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 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" 791s (fw:0, sam:1) 791s References: 791s >0 791s AGCATCGATCAGTATCTGA 791s /usr/bin/bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 15 -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 791s @HD VN:1.5 SO:unsorted GO:query 791s @SQ SN:0 LN:19 791s @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 15 -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" 791s (fw:1, sam:1) 791s References: 791s >0 791s AGCATCGATCAGTATCTGA 791s /usr/bin/bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 791s @HD VN:1.5 SO:unsorted GO:query 791s @SQ SN:0 LN:19 791s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 791s 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 791s (fw:0, sam:1) 791s References: 791s >0 791s AGCATCGATCAGTATCTGA 791s /usr/bin/bowtie2 --large-index -s 1 -u 1 --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 792s @HD VN:1.5 SO:unsorted GO:query 792s @SQ SN:0 LN:19 792s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 792s 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 792s (fw:1, sam:1) 792s References: 792s >0 792s AGCATCGATCAGTATCTGA 792s /usr/bin/bowtie2 --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 792s @HD VN:1.5 SO:unsorted GO:query 792s @SQ SN:0 LN:19 792s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 792s 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 792s (fw:0, sam:1) 792s References: 792s >0 792s AGCATCGATCAGTATCTGA 792s /usr/bin/bowtie2 --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 792s @HD VN:1.5 SO:unsorted GO:query 792s @SQ SN:0 LN:19 792s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 792s 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 792s (fw:0, sam:1) 792s References: 792s >0 792s AGCATCGATCAGTATCTGA 792s /usr/bin/bowtie2 --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 792s @HD VN:1.5 SO:unsorted GO:query 792s @SQ SN:0 LN:19 792s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 792s 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 792s (fw:1, sam:1) 792s References: 792s >0 792s AGCATCGATCAGTATCTGA 792s /usr/bin/bowtie2 --large-index -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 793s @HD VN:1.5 SO:unsorted GO:query 793s @SQ SN:0 LN:19 793s @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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 793s 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 793s (fw:1, sam:1) 793s References: 793s >0 793s TGC 793s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 794s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 794s @HD VN:1.5 SO:unsorted GO:query 794s @SQ SN:0 LN:3 794s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 794s 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 794s (fw:0, sam:1) 794s References: 794s >0 794s TGC 794s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 794s @HD VN:1.5 SO:unsorted GO:query 794s @SQ SN:0 LN:3 794s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 794s 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 794s (fw:1, sam:1) 794s References: 794s >0 794s TTGTTCGT 794s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 795s /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 795s @HD VN:1.5 SO:unsorted GO:query 795s @SQ SN:0 LN:8 795s @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" 795s 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 795s (fw:0, sam:1) 795s References: 795s >0 795s TTGTTCGT 795s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 796s @HD VN:1.5 SO:unsorted GO:query 796s @SQ SN:0 LN:8 796s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 796s 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 796s (fw:1, sam:1) 796s References: 796s >0 796s TTGTTCGT 796s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 796s @HD VN:1.5 SO:unsorted GO:query 796s @SQ SN:0 LN:8 796s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 796s 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 796s (fw:0, sam:1) 796s References: 796s >0 796s TTGTTCGT 796s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 796s @HD VN:1.5 SO:unsorted GO:query 796s @SQ SN:0 LN:8 796s @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" 796s 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 796s (fw:1, sam:1) 796s References: 796s >0 796s TTGTTCGT 796s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 796s @HD VN:1.5 SO:unsorted GO:query 796s @SQ SN:0 LN:8 796s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 796s 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 796s 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 796s (fw:0, sam:1) 796s References: 796s >0 796s TTGTTCGT 796s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 797s @HD VN:1.5 SO:unsorted GO:query 797s @SQ SN:0 LN:8 797s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 797s 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 797s 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 797s (fw:1, sam:1) 797s References: 797s >0 797s TTGTTCGT 797s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 797s @HD VN:1.5 SO:unsorted GO:query 797s @SQ SN:0 LN:8 797s @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.1a.fq.gz,.simple_tests.1b.fq.gz" 797s 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 797s 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 797s (fw:0, sam:1) 797s References: 797s >0 797s TTGTTCGT 797s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 797s @HD VN:1.5 SO:unsorted GO:query 797s @SQ SN:0 LN:8 797s @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,.simple_tests.1b.fq.gz" 797s 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 797s 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 797s (fw:1, sam:1) 797s References: 797s >0 797s TTGTTCGT 797s /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 798s @HD VN:1.5 SO:unsorted GO:query 798s @SQ SN:0 LN:8 798s @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" 798s 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 798s 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 798s 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 798s (fw:0, sam:1) 798s References: 798s >0 798s TTGTTCGT 798s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 798s @HD VN:1.5 SO:unsorted GO:query 798s @SQ SN:0 LN:8 798s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 798s 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 798s 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 798s 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 798s (fw:1, sam:1) 798s References: 798s >0 798s TTGTTCGT 798s /usr/bin/bowtie2 --large-index --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 798s @HD VN:1.5 SO:unsorted GO:query 798s @SQ SN:0 LN:8 798s @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 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" 798s 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 798s 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 798s r2 4 * 0 0 * * 0 0 GTTCGTA IIIIIII YT:Z:UU 798s r3 4 * 0 0 * * 0 0 ATTGTTC IIIIIII YT:Z:UU 798s (fw:0, sam:1) 798s References: 798s >0 798s TTGTTCGT 798s /usr/bin/bowtie2 --large-index --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,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz 799s @HD VN:1.5 SO:unsorted GO:query 799s @SQ SN:0 LN:8 799s @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 2 -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" 799s 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 799s 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 799s r2 4 * 0 0 * * 0 0 TACGAAC IIIIIII YT:Z:UU 799s r3 4 * 0 0 * * 0 0 GAACAAT IIIIIII YT:Z:UU 799s (fw:1, sam:1) 799s References: 799s >0 799s TTGTTCGT 799s /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 799s @HD VN:1.5 SO:unsorted GO:query 799s @SQ SN:0 LN:8 799s @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" 799s 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 799s (fw:0, sam:1) 799s References: 799s >0 799s TTGTTCGT 799s /usr/bin/bowtie2 --large-index --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 799s @HD VN:1.5 SO:unsorted GO:query 799s @SQ SN:0 LN:8 799s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 799s 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 799s (fw:1, sam:1) 799s References: 799s >0 799s TTGTTCGT 799s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 799s @HD VN:1.5 SO:unsorted GO:query 799s @SQ SN:0 LN:8 799s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 799s 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 799s (fw:0, sam:1) 799s References: 799s >0 799s TTGTTCGT 799s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 800s @HD VN:1.5 SO:unsorted GO:query 800s @SQ SN:0 LN:8 800s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 800s 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 800s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 800s References: 800s >0 800s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 800s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 800s /usr/bin/bowtie2 --large-index -X 1000 --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 801s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 801s @HD VN:1.5 SO:unsorted GO:query 801s @SQ SN:0 LN:1000 801s @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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 801s 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 801s 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 801s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 801s References: 801s >0 801s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 801s /usr/bin/bowtie2 --large-index -X 1000 --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 801s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 801s @HD VN:1.5 SO:unsorted GO:query 801s @SQ SN:0 LN:1000 801s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 801s 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 801s 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 801s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 801s References: 801s >0 801s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 801s /usr/bin/bowtie2 --large-index -X 1000 --local --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 801s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 801s @HD VN:1.5 SO:unsorted GO:query 801s @SQ SN:0 LN:1000 801s @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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 801s 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 801s 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 801s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 801s References: 801s >0 801s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 801s /usr/bin/bowtie2 --large-index -X 1000 --local --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 801s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 801s @HD VN:1.5 SO:unsorted GO:query 801s @SQ SN:0 LN:1000 801s @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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 801s 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 801s 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 801s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 801s References: 801s >0 801s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 801s /usr/bin/bowtie2 --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 802s @HD VN:1.5 SO:unsorted GO:query 802s @SQ SN:0 LN:1000 802s @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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 802s References: 802s >0 802s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 802s /usr/bin/bowtie2 --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 802s @HD VN:1.5 SO:unsorted GO:query 802s @SQ SN:0 LN:1000 802s @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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 802s References: 802s >0 802s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 802s /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 802s @HD VN:1.5 SO:unsorted GO:query 802s @SQ SN:0 LN:1000 802s @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" 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 802s References: 802s >0 802s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 802s /usr/bin/bowtie2 --large-index -X 1000 --local --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 802s @HD VN:1.5 SO:unsorted GO:query 802s @SQ SN:0 LN:1000 802s @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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s 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 802s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 802s References: 802s >0 802s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 802s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 803s /usr/bin/bowtie2 --large-index -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 803s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 803s @HD VN:1.5 SO:unsorted GO:query 803s @SQ SN:0 LN:363 803s @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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 803s 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 803s 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 803s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 803s References: 804s >0 804s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 804s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 804s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 804s @HD VN:1.5 SO:unsorted GO:query 804s @SQ SN:0 LN:363 804s @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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 804s 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 804s 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 804s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 804s References: 804s >0 804s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 804s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 804s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 804s @HD VN:1.5 SO:unsorted GO:query 804s @SQ SN:0 LN:363 804s @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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 804s 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 804s 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 804s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 804s References: 804s >0 804s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 804s /usr/bin/bowtie2 --large-index --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 804s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 804s @HD VN:1.5 SO:unsorted GO:query 804s @SQ SN:0 LN:363 804s @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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 804s 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 804s 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 804s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 804s References: 804s >0 804s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 804s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 805s @HD VN:1.5 SO:unsorted GO:query 805s @SQ SN:0 LN:363 805s @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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 805s 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 805s 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 805s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 805s References: 805s >0 805s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 805s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 806s @HD VN:1.5 SO:unsorted GO:query 806s @SQ SN:0 LN:363 806s @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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 806s 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 806s 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 806s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 806s References: 806s >0 806s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 806s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 806s @HD VN:1.5 SO:unsorted GO:query 806s @SQ SN:0 LN:363 806s @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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 806s 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 806s 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 806s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 806s References: 806s >0 806s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 806s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 806s @HD VN:1.5 SO:unsorted GO:query 806s @SQ SN:0 LN:363 806s @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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 806s 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 806s 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 806s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 806s References: 806s >0 806s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 806s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 806s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 806s @HD VN:1.5 SO:unsorted GO:query 806s @SQ SN:0 LN:363 806s @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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 806s 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 806s 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 806s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 806s References: 806s >0 806s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 806s /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 806s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 806s @HD VN:1.5 SO:unsorted GO:query 806s @SQ SN:0 LN:363 806s @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" 806s 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 806s 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 806s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 806s References: 806s >0 806s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 806s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --local -X 150 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 806s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 806s @HD VN:1.5 SO:unsorted GO:query 806s @SQ SN:0 LN:363 806s @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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 806s 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 806s 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 806s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 806s References: 806s >0 806s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 806s /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 806s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 806s @HD VN:1.5 SO:unsorted GO:query 806s @SQ SN:0 LN:363 806s @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" 806s 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 806s 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 806s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 806s References: 806s >0 806s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 806s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 807s /usr/bin/bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 808s @HD VN:1.5 SO:unsorted GO:query 808s @SQ SN:0 LN:126 808s @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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 808s 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 808s 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 808s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 808s References: 808s >0 808s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 808s /usr/bin/bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 808s @HD VN:1.5 SO:unsorted GO:query 808s @SQ SN:0 LN:126 808s @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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 808s 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 808s 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 808s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 808s References: 808s >0 808s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 808s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 808s @HD VN:1.5 SO:unsorted GO:query 808s @SQ SN:0 LN:126 808s @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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 808s 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 808s 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 808s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 808s References: 808s >0 808s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 808s /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 808s @HD VN:1.5 SO:unsorted GO:query 808s @SQ SN:0 LN:126 808s @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" 808s 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 808s 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 808s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 808s References: 808s >0 808s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 808s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 809s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 809s @HD VN:1.5 SO:unsorted GO:query 809s @SQ SN:0 LN:126 809s @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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 809s 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 809s 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 809s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 809s References: 809s >0 809s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 809s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 809s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 809s @HD VN:1.5 SO:unsorted GO:query 809s @SQ SN:0 LN:126 809s @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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 809s 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 809s 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 809s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 809s References: 809s >0 809s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 809s /usr/bin/bowtie2 --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 809s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 809s @HD VN:1.5 SO:unsorted GO:query 809s @SQ SN:0 LN:126 809s @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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 809s 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 809s 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 809s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 809s References: 809s >0 809s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 809s /usr/bin/bowtie2 --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 809s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 810s @HD VN:1.5 SO:unsorted GO:query 810s @SQ SN:0 LN:126 810s @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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 810s 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 810s 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 810s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 810s References: 810s >0 810s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 810s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 810s /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 811s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 811s @HD VN:1.5 SO:unsorted GO:query 811s @SQ SN:0 LN:2607 811s @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" 811s 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 811s 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 811s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 811s References: 811s >0 811s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 811s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 811s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 811s @HD VN:1.5 SO:unsorted GO:query 811s @SQ SN:0 LN:2607 811s @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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 811s 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 811s 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 811s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:1, sam:1) 811s References: 811s >0 811s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 811s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 812s /usr/bin/bowtie2 --large-index --local -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 812s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 812s @HD VN:1.5 SO:unsorted GO:query 812s @SQ SN:0 LN:1906 812s @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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 812s 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 812s 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 812s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1) 812s References: 812s >0 812s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 812s /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 812s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 812s @HD VN:1.5 SO:unsorted GO:query 812s @SQ SN:0 LN:1906 812s @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" 812s 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 812s 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 812s U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1) 812s References: 813s >0 813s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 813s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 813s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 814s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 814s @HD VN:1.5 SO:unsorted GO:query 814s @SQ SN:0 LN:56 814s @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" 814s 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 814s U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1) 814s References: 814s >0 814s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 814s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 814s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 814s @HD VN:1.5 SO:unsorted GO:query 814s @SQ SN:0 LN:56 814s @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" 814s 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 814s U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1) 814s References: 814s >0 814s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 814s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 814s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 814s @HD VN:1.5 SO:unsorted GO:query 814s @SQ SN:0 LN:56 814s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 814s 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 814s U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1) 814s References: 814s >0 814s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 814s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 814s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 814s @HD VN:1.5 SO:unsorted GO:query 814s @SQ SN:0 LN:56 814s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 814s 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 814s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1) 814s References: 814s >0 814s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 814s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 815s @HD VN:1.5 SO:unsorted GO:query 815s @SQ SN:0 LN:56 815s @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" 815s 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 815s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1) 815s References: 815s >0 815s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 815s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 815s @HD VN:1.5 SO:unsorted GO:query 815s @SQ SN:0 LN:56 815s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 815s 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 815s U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1) 815s References: 815s >0 815s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 815s /usr/bin/bowtie2 --large-index --local --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 815s @HD VN:1.5 SO:unsorted GO:query 815s @SQ SN:0 LN:56 815s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 815s 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 815s U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1) 815s References: 815s >0 815s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 815s /usr/bin/bowtie2 --large-index --local --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 816s @HD VN:1.5 SO:unsorted GO:query 816s @SQ SN:0 LN:56 816s @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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 816s 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 816s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1) 816s References: 816s >0 816s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 816s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 816s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 817s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 817s @HD VN:1.5 SO:unsorted GO:query 817s @SQ SN:0 LN:85 817s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 817s 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 817s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1) 817s References: 817s >0 817s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 817s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 817s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 817s @HD VN:1.5 SO:unsorted GO:query 817s @SQ SN:0 LN:85 817s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 817s 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 817s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1) 817s References: 817s >0 817s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 817s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 817s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 817s @HD VN:1.5 SO:unsorted GO:query 817s @SQ SN:0 LN:85 817s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 817s 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 817s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) 817s References: 817s >0 817s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 817s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 817s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 818s @HD VN:1.5 SO:unsorted GO:query 818s @SQ SN:0 LN:85 818s @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" 818s 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 818s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1) 818s References: 818s >0 818s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 818s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 818s @HD VN:1.5 SO:unsorted GO:query 818s @SQ SN:0 LN:85 818s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 818s 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 818s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) 818s References: 818s >0 818s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 818s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 818s @HD VN:1.5 SO:unsorted GO:query 818s @SQ SN:0 LN:85 818s @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" 818s 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 818s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1) 818s References: 818s >0 818s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 818s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 818s @HD VN:1.5 SO:unsorted GO:query 818s @SQ SN:0 LN:85 818s @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" 818s 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 818s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) 818s References: 818s >0 818s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 818s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 819s @HD VN:1.5 SO:unsorted GO:query 819s @SQ SN:0 LN:85 819s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 819s 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 819s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1) 819s References: 819s >0 819s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 819s /usr/bin/bowtie2 --large-index --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 819s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 819s @HD VN:1.5 SO:unsorted GO:query 819s @SQ SN:0 LN:85 819s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 819s 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 819s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1) 819s References: 819s >0 819s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 819s /usr/bin/bowtie2 --large-index --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 819s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 819s @HD VN:1.5 SO:unsorted GO:query 819s @SQ SN:0 LN:85 819s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 819s 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 819s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1) 819s References: 819s >0 819s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 819s /usr/bin/bowtie2 --large-index --quiet -M 2 --local --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 819s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 819s @HD VN:1.5 SO:unsorted GO:query 819s @SQ SN:0 LN:85 819s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 819s 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 819s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1) 819s References: 819s >0 819s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 820s /usr/bin/bowtie2 --large-index --quiet -M 2 --local --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 820s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 820s @HD VN:1.5 SO:unsorted GO:query 820s @SQ SN:0 LN:85 820s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 820s 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 820s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1) 820s References: 820s >0 820s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 820s /usr/bin/bowtie2 --large-index --quiet -k 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 820s @HD VN:1.5 SO:unsorted GO:query 820s @SQ SN:0 LN:85 820s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 820s 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 820s 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 820s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1) 820s References: 820s >0 820s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 820s /usr/bin/bowtie2 --large-index --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 820s @HD VN:1.5 SO:unsorted GO:query 820s @SQ SN:0 LN:85 820s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 820s 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 820s 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 820s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1) 820s References: 820s >0 820s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 820s /usr/bin/bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 821s @HD VN:1.5 SO:unsorted GO:query 821s @SQ SN:0 LN:85 821s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 821s 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 821s 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 821s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1) 821s References: 821s >0 821s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 821s /usr/bin/bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 821s @HD VN:1.5 SO:unsorted GO:query 821s @SQ SN:0 LN:85 821s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 821s 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 821s 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 821s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 821s References: 821s >0 821s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 821s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 822s /usr/bin/bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 822s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 822s @HD VN:1.5 SO:unsorted GO:query 822s @SQ SN:0 LN:340 822s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 822s 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 822s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 822s References: 822s >0 822s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 822s /usr/bin/bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 822s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 822s @HD VN:1.5 SO:unsorted GO:query 822s @SQ SN:0 LN:340 822s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 822s 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 822s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 822s References: 822s >0 822s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 822s /usr/bin/bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 823s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 823s @HD VN:1.5 SO:unsorted GO:query 823s @SQ SN:0 LN:340 823s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 823s 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 823s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 823s References: 823s >0 823s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 823s /usr/bin/bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 823s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 823s @HD VN:1.5 SO:unsorted GO:query 823s @SQ SN:0 LN:340 823s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 823s 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 823s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1) 823s References: 823s >0 823s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 823s /usr/bin/bowtie2 --large-index --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 823s @HD VN:1.5 SO:unsorted GO:query 823s @SQ SN:0 LN:340 823s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 823s 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 823s 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 823s 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 823s 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 823s 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 823s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:0, sam:1) 823s References: 823s >0 823s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 823s /usr/bin/bowtie2 --large-index --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 823s @HD VN:1.5 SO:unsorted GO:query 823s @SQ SN:0 LN:340 823s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 823s 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 823s 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 823s 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 823s 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 823s 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 823s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:1, sam:1) 823s References: 823s >0 823s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 823s /usr/bin/bowtie2 --large-index --local --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 824s @HD VN:1.5 SO:unsorted GO:query 824s @SQ SN:0 LN:340 824s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 824s 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 824s 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 824s 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 824s 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 824s 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 824s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:0, sam:1) 824s References: 824s >0 824s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 824s /usr/bin/bowtie2 --large-index --local --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 824s @HD VN:1.5 SO:unsorted GO:query 824s @SQ SN:0 LN:340 824s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 824s 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 824s 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 824s 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 824s 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 824s 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 824s (fw:1, sam:1) 824s References: 824s >0 824s TTGTTCGTTTGTTCGT 824s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 825s /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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 825s @HD VN:1.5 SO:unsorted GO:query 825s @SQ SN:0 LN:16 825s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 825s 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 825s 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 825s (fw:0, sam:1) 825s References: 825s >0 825s TTGTTCGTTTGTTCGT 825s /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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 825s @HD VN:1.5 SO:unsorted GO:query 825s @SQ SN:0 LN:16 825s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 825s 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 825s 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 825s (fw:1, sam:1) 825s References: 825s >0 825s TTGTTCGTTTGTTCGT 825s /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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 826s @HD VN:1.5 SO:unsorted GO:query 826s @SQ SN:0 LN:16 826s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 826s r0 4 * 0 0 * * 0 0 TTGTTCAT IIIIIIII YT:Z:UU 826s (fw:0, sam:1) 826s References: 826s >0 826s TTGTTCGTTTGTTCGT 826s /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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 826s @HD VN:1.5 SO:unsorted GO:query 826s @SQ SN:0 LN:16 826s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 826s r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU 826s (fw:1, sam:1) 826s References: 826s >0 826s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 826s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 827s /usr/bin/bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 12 -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 827s @HD VN:1.5 SO:unsorted GO:query 827s @SQ SN:0 LN:49 827s @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 12 -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" 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s 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 827s (fw:0, sam:1) 827s References: 827s >0 827s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 827s /usr/bin/bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 16 -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 828s @HD VN:1.5 SO:unsorted GO:query 828s @SQ SN:0 LN:49 828s @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 16 -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" 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s 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 828s Gap penalties 1 (fw:1, sam:1) 828s References: 828s >0 828s TTGTTCGTTTGTTCGT 828s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 828s /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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 829s @HD VN:1.5 SO:unsorted GO:query 829s @SQ SN:0 LN:16 829s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 829s 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 829s Gap penalties 1 (fw:0, sam:1) 829s References: 829s >0 829s TTGTTCGTTTGTTCGT 829s /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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 829s @HD VN:1.5 SO:unsorted GO:query 829s @SQ SN:0 LN:16 829s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 829s 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 829s Gap penalties 2 (fw:1, sam:1) 829s References: 829s >0 829s TTGTTCGTTTGTTCGT 829s /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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 829s @HD VN:1.5 SO:unsorted GO:query 829s @SQ SN:0 LN:16 829s @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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 829s r0 4 * 0 0 * * 0 0 TTGTTCTTTGTT IIIIIIIIIIII YT:Z:UU 829s Gap penalties 2 (fw:0, sam:1) 829s References: 829s >0 829s TTGTTCGTTTGTTCGT 829s /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 830s @HD VN:1.5 SO:unsorted GO:query 830s @SQ SN:0 LN:16 830s @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" 830s r0 4 * 0 0 * * 0 0 AACAAAGAACAA IIIIIIIIIIII YT:Z:UU 830s Gap penalties 3 (fw:1, sam:1) 830s References: 830s >0 830s TTGTTCGTTTGTTCGT 830s /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 830s @HD VN:1.5 SO:unsorted GO:query 830s @SQ SN:0 LN:16 830s @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" 830s 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 830s Gap penalties 3 (fw:0, sam:1) 830s References: 830s >0 830s TTGTTCGTTTGTTCGT 830s /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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 830s @HD VN:1.5 SO:unsorted GO:query 830s @SQ SN:0 LN:16 830s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 830s 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 830s Gap penalties 4 (fw:1, sam:1) 830s References: 830s >0 830s TTGTTCGTTTGTTCGT 830s /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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 831s @HD VN:1.5 SO:unsorted GO:query 831s @SQ SN:0 LN:16 831s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 831s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 831s Gap penalties 4 (fw:0, sam:1) 831s References: 831s >0 831s TTGTTCGTTTGTTCGT 831s /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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 831s @HD VN:1.5 SO:unsorted GO:query 831s @SQ SN:0 LN:16 831s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 831s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 831s Gap penalties 5 (fw:1, sam:1) 831s References: 831s >0 831s TTGTTCGTTTGTTCGT 831s /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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 831s @HD VN:1.5 SO:unsorted GO:query 831s @SQ SN:0 LN:16 831s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 831s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 831s Gap penalties 5 (fw:0, sam:1) 831s References: 831s >0 831s TTGTTCGTTTGTTCGT 831s /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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 831s @HD VN:1.5 SO:unsorted GO:query 831s @SQ SN:0 LN:16 831s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 831s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 831s Gap penalties 6 (fw:1, sam:1) 831s References: 831s >0 831s ATTGTTCGTTTGTTCGTA 831s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 832s /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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 833s @HD VN:1.5 SO:unsorted GO:query 833s @SQ SN:0 LN:18 833s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 833s 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 833s Gap penalties 6 (fw:0, sam:1) 833s References: 833s >0 833s ATTGTTCGTTTGTTCGTA 833s /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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 833s @HD VN:1.5 SO:unsorted GO:query 833s @SQ SN:0 LN:18 833s @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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 833s 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 833s Gap penalties 7 (fw:1, sam:1) 833s References: 833s >0 833s TTGTTCGTTTGTTCGT 833s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 834s /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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 834s @HD VN:1.5 SO:unsorted GO:query 834s @SQ SN:0 LN:16 834s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 834s r0 4 * 0 0 * * 0 0 TTGTTGTTTGATTCGT IIIIIIIIIIIIIIII YT:Z:UU 834s Gap penalties 7 (fw:0, sam:1) 834s References: 834s >0 834s TTGTTCGTTTGTTCGT 834s /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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 834s @HD VN:1.5 SO:unsorted GO:query 834s @SQ SN:0 LN:16 834s @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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 834s r0 4 * 0 0 * * 0 0 ACGAATCAAACAACAA IIIIIIIIIIIIIIII YT:Z:UU 834s N filtering 1 (fw:1, sam:1) 834s References: 834s >0 834s GAGACTTTATACGCATCGAACTATCGCTCTA 834s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 835s /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 835s @HD VN:1.5 SO:unsorted GO:query 835s @SQ SN:0 LN:31 835s @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" 835s 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 835s N filtering 1 (fw:0, sam:1) 835s References: 835s >0 835s GAGACTTTATACGCATCGAACTATCGCTCTA 835s /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 836s @HD VN:1.5 SO:unsorted GO:query 836s @SQ SN:0 LN:31 836s @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" 836s 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 836s N filtering 2 (fw:1, sam:1) 836s References: 836s >0 836s GAGACTTTATNCGCATCGAACTATCGCTCTA 836s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 837s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 837s @HD VN:1.5 SO:unsorted GO:query 837s @SQ SN:0 LN:31 837s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 837s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 837s N filtering 2 (fw:0, sam:1) 837s References: 837s >0 837s GAGACTTTATNCGCATCGAACTATCGCTCTA 837s /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 837s @HD VN:1.5 SO:unsorted GO:query 837s @SQ SN:0 LN:31 837s @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" 837s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 837s N filtering 3 (fw:1, sam:1) 837s References: 837s >0 837s GAGACTTTATACGCATCGAANTATCGCTCTA 837s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 838s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 838s @HD VN:1.5 SO:unsorted GO:query 838s @SQ SN:0 LN:31 838s @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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 838s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 838s N filtering 3 (fw:0, sam:1) 838s References: 838s >0 838s GAGACTTTATACGCATCGAANTATCGCTCTA 838s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 838s @HD VN:1.5 SO:unsorted GO:query 838s @SQ SN:0 LN:31 838s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 838s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 838s N filtering 4 (fw:1, sam:1) 838s References: 838s >0 838s GAGACTTTNTACGCATCGAACTATCGCTCTA 838s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 839s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 840s @HD VN:1.5 SO:unsorted GO:query 840s @SQ SN:0 LN:31 840s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 840s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 840s N filtering 4 (fw:0, sam:1) 840s References: 840s >0 840s GAGACTTTNTACGCATCGAACTATCGCTCTA 840s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 840s @HD VN:1.5 SO:unsorted GO:query 840s @SQ SN:0 LN:31 840s @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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 840s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 840s N filtering 5 (fw:1, sam:1) 840s References: 840s >0 840s GAGACTTTATNCGCATCGAACTATCGCTCTA 840s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 841s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 841s @HD VN:1.5 SO:unsorted GO:query 841s @SQ SN:0 LN:31 841s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 841s 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 841s N filtering 5 (fw:0, sam:1) 841s References: 841s >0 841s GAGACTTTATNCGCATCGAACTATCGCTCTA 841s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 841s @HD VN:1.5 SO:unsorted GO:query 841s @SQ SN:0 LN:31 841s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 841s 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 841s N filtering 6 (fw:1, sam:1) 841s References: 841s >0 841s GAGACTTTNTACGCATCGAANTATCGCTCTA 841s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 842s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 842s @HD VN:1.5 SO:unsorted GO:query 842s @SQ SN:0 LN:31 842s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 842s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 842s N filtering 6 (fw:0, sam:1) 842s References: 842s >0 842s GAGACTTTNTACGCATCGAANTATCGCTCTA 843s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 843s @HD VN:1.5 SO:unsorted GO:query 843s @SQ SN:0 LN:31 843s @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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 843s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 843s (fw:1, sam:1) 843s References: 843s >0 843s TTTTGTTCGTTTG 843s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 844s /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 844s @HD VN:1.5 SO:unsorted GO:query 844s @SQ SN:0 LN:13 844s @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" 844s 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 844s (fw:0, sam:1) 844s References: 844s >0 844s TTTTGTTCGTTTG 844s /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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 844s @HD VN:1.5 SO:unsorted GO:query 844s @SQ SN:0 LN:13 844s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 844s 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 844s (fw:1, sam:1) 844s References: 844s >0 844s TTGTTCGTTTGTT 844s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 845s /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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 845s @HD VN:1.5 SO:unsorted GO:query 845s @SQ SN:0 LN:13 845s @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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 845s 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 845s (fw:0, sam:1) 845s References: 845s >0 845s TTGTTCGTTTGTT 845s /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 846s @HD VN:1.5 SO:unsorted GO:query 846s @SQ SN:0 LN:13 846s @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" 846s 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 846s (fw:1, sam:1) 846s References: 846s >0 846s ACNCA 846s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 847s /usr/bin/bowtie2 --large-index --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 847s @HD VN:1.5 SO:unsorted GO:query 847s @SQ SN:0 LN:5 847s @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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 847s 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 847s (fw:0, sam:1) 847s References: 847s >0 847s ACNCA 847s /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 847s @HD VN:1.5 SO:unsorted GO:query 847s @SQ SN:0 LN:5 847s @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" 847s 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 847s N ceil = 0, 2 legit hits (1) (fw:1, sam:1) 847s References: 847s >0 847s ACNCA 847s /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 847s @HD VN:1.5 SO:unsorted GO:query 847s @SQ SN:0 LN:5 847s @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" 847s 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 847s N ceil = 0, 2 legit hits (1) (fw:0, sam:1) 847s References: 847s >0 847s ACNCA 847s /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 848s @HD VN:1.5 SO:unsorted GO:query 848s @SQ SN:0 LN:5 848s @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" 848s 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 848s N ceil = 0, 2 legit hits (2) (fw:1, sam:1) 848s References: 848s >0 848s ACNCANNNNNNNNCGNNNNNNNNCG 848s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 849s /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 849s @HD VN:1.5 SO:unsorted GO:query 849s @SQ SN:0 LN:25 849s @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" 849s 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 849s 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 849s 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 849s 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 849s N ceil = 0, 2 legit hits (2) (fw:0, sam:1) 849s References: 849s >0 849s ACNCANNNNNNNNCGNNNNNNNNCG 849s /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 849s @HD VN:1.5 SO:unsorted GO:query 849s @SQ SN:0 LN:25 849s @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" 849s 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 849s 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 849s 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 849s 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 849s (fw:1, sam:1) 849s References: 849s >0 849s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 849s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 850s /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 850s @HD VN:1.5 SO:unsorted GO:query 850s @SQ SN:0 LN:37 850s @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" 850s 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 850s 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 850s 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 850s 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 850s 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 850s 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 850s (fw:0, sam:1) 850s References: 850s >0 850s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 850s /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 851s @HD VN:1.5 SO:unsorted GO:query 851s @SQ SN:0 LN:37 851s @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" 851s 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 851s 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 851s 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 851s 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 851s 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 851s 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 851s (fw:1, sam:1) 851s References: 851s >0 851s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 851s /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 851s @HD VN:1.5 SO:unsorted GO:query 851s @SQ SN:0 LN:37 851s @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" 851s 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 851s 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 851s 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 851s 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 851s 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 851s 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 851s (fw:0, sam:1) 851s References: 851s >0 851s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 851s /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 851s @HD VN:1.5 SO:unsorted GO:query 851s @SQ SN:0 LN:37 851s @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" 851s 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 851s 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 851s 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 851s 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 851s 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 851s 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 851s (fw:1, sam:1) 851s References: 851s >0 851s TTGTTYGT 851s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 852s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 852s @HD VN:1.5 SO:unsorted GO:query 852s @SQ SN:0 LN:8 852s @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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 852s 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 852s 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 852s (fw:1, sam:1) 852s References: 852s >0 852s ATAACCTTCG 852s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 853s /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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 854s @HD VN:1.5 SO:unsorted GO:query 854s @SQ SN:0 LN:10 854s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 854s 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 854s (fw:0, sam:1) 854s References: 854s >0 854s ATAACCTTCG 854s /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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 854s @HD VN:1.5 SO:unsorted GO:query 854s @SQ SN:0 LN:10 854s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 854s 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 854s (fw:1, sam:1) 854s References: 854s >0 854s ATATGCCCCATGCCCCCCTCCG 854s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 855s /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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 855s @HD VN:1.5 SO:unsorted GO:query 855s @SQ SN:0 LN:22 855s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 855s 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 855s (fw:1, sam:1) 855s References: 855s >0 855s ATATGCCCCATGCCCCCCTCCG 855s /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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 855s @HD VN:1.5 SO:unsorted GO:query 855s @SQ SN:0 LN:22 855s @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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 855s 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 855s Simple paired-end 13 (fw:1, sam:1) 855s References: 855s >0 855s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 855s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 856s /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 857s @HD VN:1.5 SO:unsorted GO:query 857s @SQ SN:0 LN:51 857s @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" 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s Simple paired-end 13 (fw:0, sam:1) 857s References: 857s >0 857s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 857s /usr/bin/bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 5 -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 857s @HD VN:1.5 SO:unsorted GO:query 857s @SQ SN:0 LN:51 857s @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 5 -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" 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s 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 857s Simple paired-end 12 (fw:1, sam:1) 857s References: 857s >0 857s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 857s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 858s /usr/bin/bowtie2 --large-index -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 858s @HD VN:1.5 SO:unsorted GO:query 858s @SQ SN:0 LN:51 858s @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 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" 858s 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 858s 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 858s 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 858s 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 858s Simple paired-end 12 (fw:0, sam:1) 858s References: 858s >0 858s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 858s /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,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 859s @HD VN:1.5 SO:unsorted GO:query 859s @SQ SN:0 LN:51 859s @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,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 859s 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 859s 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 859s 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 859s 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 859s Simple paired-end 11 (fw:1, sam:1) 859s References: 859s >0 859s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 859s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 860s /usr/bin/bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 860s @HD VN:1.5 SO:unsorted GO:query 860s @SQ SN:0 LN:51 860s @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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 860s 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 860s 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 860s Simple paired-end 11 (fw:0, sam:1) 860s References: 860s >0 860s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 860s /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 860s @HD VN:1.5 SO:unsorted GO:query 860s @SQ SN:0 LN:51 860s @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" 860s 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 860s 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 860s Simple paired-end 10 (fw:1, sam:1) 860s References: 860s >0 860s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 860s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 861s /usr/bin/bowtie2 --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 862s @HD VN:1.5 SO:unsorted GO:query 862s @SQ SN:0 LN:41 862s @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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 862s 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 862s 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 862s Simple paired-end 10 (fw:0, sam:1) 862s References: 862s >0 862s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 862s /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 862s @HD VN:1.5 SO:unsorted GO:query 862s @SQ SN:0 LN:41 862s @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" 862s 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 862s 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 862s Simple paired-end 9 (fw:1, sam:1) 862s References: 862s >0 862s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 862s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 863s /usr/bin/bowtie2 --large-index -I 0 -X 80 --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 863s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 863s @HD VN:1.5 SO:unsorted GO:query 863s @SQ SN:0 LN:81 863s @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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 863s 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 863s 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 863s Simple paired-end 9 (fw:0, sam:1) 863s References: 863s >0 863s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 863s /usr/bin/bowtie2 --large-index -I 0 -X 80 --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 863s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 863s @HD VN:1.5 SO:unsorted GO:query 863s @SQ SN:0 LN:81 863s @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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 863s 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 863s 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 863s Simple paired-end 8 (fw:1, sam:1) 863s References: 863s >0 863s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 863s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 864s /usr/bin/bowtie2 --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 864s @HD VN:1.5 SO:unsorted GO:query 864s @SQ SN:0 LN:81 864s @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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 864s 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 864s 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 864s 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 864s 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 864s 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 864s 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 865s Simple paired-end 8 (fw:0, sam:1) 865s References: 865s >0 865s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 865s /usr/bin/bowtie2 --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 865s @HD VN:1.5 SO:unsorted GO:query 865s @SQ SN:0 LN:81 865s @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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 865s 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 865s 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 865s 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 865s 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 865s 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 865s 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 865s Simple paired-end 2; no --no-mixed (fw:0, sam:1) 865s References: 865s >0 865s CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC 865s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 866s /usr/bin/bowtie2 --large-index -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 866s @HD VN:1.5 SO:unsorted GO:query 866s @SQ SN:0 LN:53 866s @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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 866s 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 866s r0 101 0 4 0 * = 4 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 866s Simple paired-end 2; --no-mixed (fw:1, sam:1) 866s References: 866s >0 866s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 866s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 867s /usr/bin/bowtie2 --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 867s @HD VN:1.5 SO:unsorted GO:query 867s @SQ SN:0 LN:53 867s @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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 867s r0 77 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 867s r0 141 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 867s Simple paired-end 2; --no-mixed (fw:0, sam:1) 867s References: 867s >0 867s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 867s /usr/bin/bowtie2 --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 868s @HD VN:1.5 SO:unsorted GO:query 868s @SQ SN:0 LN:53 868s @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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 868s r0 77 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 868s r0 141 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 868s Simple paired-end 1 (fw:1, sam:1) 868s References: 868s >0 868s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 868s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 869s /usr/bin/bowtie2 --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 869s @HD VN:1.5 SO:unsorted GO:query 869s @SQ SN:0 LN:53 869s @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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 869s 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 869s 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 869s Simple paired-end 1 (fw:0, sam:1) 869s References: 869s >0 869s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 869s /usr/bin/bowtie2 --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 869s @HD VN:1.5 SO:unsorted GO:query 869s @SQ SN:0 LN:53 869s @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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 869s 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 869s 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 869s (fw:1, sam:1) 869s References: 869s >0 869s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 869s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 870s /usr/bin/bowtie2 --large-index --quiet -k 1 --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,.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 871s @HD VN:1.5 SO:unsorted GO:query 871s @SQ SN:0 LN:49 871s @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,.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" 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s (fw:0, sam:1) 871s References: 871s >0 871s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 871s /usr/bin/bowtie2 --large-index --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 871s @HD VN:1.5 SO:unsorted GO:query 871s @SQ SN:0 LN:49 871s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --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" 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s 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 871s (fw:1, sam:1) 871s References: 871s >0 871s TTGTTCGTTTGTTCGT 871s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 872s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 872s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 872s @HD VN:1.5 SO:unsorted GO:query 872s @SQ SN:0 LN:16 872s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 872s 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 872s (fw:0, sam:1) 872s References: 872s >0 872s TTGTTCGTTTGTTCGT 872s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 873s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 873s @HD VN:1.5 SO:unsorted GO:query 873s @SQ SN:0 LN:16 873s @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" 873s 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 873s (fw:1, sam:1) 873s References: 873s >0 873s TTGTTCGT 873s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 874s /usr/bin/bowtie2 --large-index --overhang --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 874s @HD VN:1.5 SO:unsorted GO:query 874s @SQ SN:0 LN:8 874s @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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 874s 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 874s (fw:0, sam:1) 874s References: 874s >0 874s TTGTTCGT 874s /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 874s @HD VN:1.5 SO:unsorted GO:query 874s @SQ SN:0 LN:8 874s @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" 874s 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 874s (fw:1, sam:1) 874s References: 874s >0 874s TTGTTCGTTTGTTCGT 874s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 875s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 875s @HD VN:1.5 SO:unsorted GO:query 875s @SQ SN:0 LN:16 875s @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 -q .simple_tests.1a.fq.gz" 875s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 875s (fw:0, sam:1) 875s References: 875s >0 875s TTGTTCGTTTGTTCGT 875s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 876s @HD VN:1.5 SO:unsorted GO:query 876s @SQ SN:0 LN:16 876s @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" 876s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 876s (fw:1, sam:1) 876s References: 876s >0 876s TTGTTCGTTTGTTCGT 876s /usr/bin/bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 876s @HD VN:1.5 SO:unsorted GO:query 876s @SQ SN:0 LN:16 876s @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" 876s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 876s (fw:0, sam:1) 876s References: 876s >0 876s TTGTTCGTTTGTTCGT 876s /usr/bin/bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 876s @HD VN:1.5 SO:unsorted GO:query 876s @SQ SN:0 LN:16 876s @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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 876s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 876s (fw:1, sam:1) 876s References: 876s >0 876s TTGTTCGTTTGTTCGT 876s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 876s @HD VN:1.5 SO:unsorted GO:query 876s @SQ SN:0 LN:16 876s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 876s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 876s (fw:0, sam:1) 876s References: 876s >0 876s TTGTTCGTTTGTTCGT 876s /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 877s @HD VN:1.5 SO:unsorted GO:query 877s @SQ SN:0 LN:16 877s @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" 877s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 877s (fw:1, sam:1) 877s References: 877s >0 877s TTGTTCGTTTGTTCGT 877s /usr/bin/bowtie2 --large-index --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 877s @HD VN:1.5 SO:unsorted GO:query 877s @SQ SN:0 LN:16 877s @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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 877s 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 877s 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 877s 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 877s 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 877s 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 877s 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 877s (fw:0, sam:1) 877s References: 877s >0 877s TTGTTCGTTTGTTCGT 877s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 877s @HD VN:1.5 SO:unsorted GO:query 877s @SQ SN:0 LN:16 877s @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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 877s 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 877s 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 877s 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 877s 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 877s 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 877s 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 877s PASSED 878s Created DNA generator 878s N frac: 0.035 878s IUPAC frac: 0.002 878s AT/ACGT frac: 0.428 878s A/AT frac: 0.629 878s C/CG frac: 0.345 878s Generating 2 references 878s Generated reference 'Sim.pm.1' of untrimmed length 122, trimmed length 24 878s Generated reference 'Sim.pm.2' of untrimmed length 249, trimmed length 50 878s Wrote references to /tmp/Sim.pm.77cQkkTL.fa 878s A: 23 878s C: 15 878s G: 23 878s T: 13 878s Executing: /usr/bin/bowtie2-build --threads 1 --offrate 7 /tmp/Sim.pm.77cQkkTL.fa /tmp/Sim.pm.77cQkkTL 878s *** TEST CASE *** 878s Settings: 878s Output files: "/tmp/Sim.pm.77cQkkTL.*.bt2" 878s Line rate: 6 (line is 64 bytes) 878s Building a SMALL index Lines per side: 1 (side is 64 bytes) 878s Offset rate: 7 (one in 128) 878s FTable chars: 10 878s Strings: unpacked 878s Max bucket size: default 878s Max bucket size, sqrt multiplier: default 878s Max bucket size, len divisor: 4 878s Difference-cover sample period: 1024 878s Endianness: little 878s Actual local endianness: little 878s Sanity checking: disabled 878s Assertions: disabled 878s Random seed: 0 878s Sizeofs: void*:8, int:4, long:8, size_t:8 878s Input files DNA, FASTA: 878s /tmp/Sim.pm.77cQkkTL.fa 878s 878s Reading reference sizes 878s Time reading reference sizes: 00:00:00 878s Calculating joined length 878s Writing header 878s Reserving space for joined string 878s Joining reference sequences 878s Time to join reference sequences: 00:00:00 878s bmax according to bmaxDivN setting: 18 878s Using parameters --bmax 14 --dcv 1024 878s Doing ahead-of-time memory usage test 878s Passed! Constructing with these parameters: --bmax 14 --dcv 1024 878s Constructing suffix-array element generator 878s Building DifferenceCoverSample 878s Building sPrime 878s Building sPrimeOrder 878s V-Sorting samples 878s V-Sorting samples time: 00:00:00 878s Allocating rank array 878s Ranking v-sort output 878s Ranking v-sort output time: 00:00:00 878s Invoking Larsson-Sadakane on ranks 878s Invoking Larsson-Sadakane on ranks time: 00:00:00 878s Sanity-checking and returning 878s Building samples 878s Reserving space for 12 sample suffixes 878s Generating random suffixes 878s QSorting 12 sample offsets, eliminating duplicates 878s QSorting sample offsets, eliminating duplicates time: 00:00:00 878s Multikey QSorting 9 samples 878s (Using difference cover) 878s Multikey QSorting samples time: 00:00:00 878s Calculating bucket sizes 878s Splitting and merging 878s Splitting and merging time: 00:00:00 878s Split 2, merged 4; iterating... 878s Splitting and merging 878s Splitting and merging time: 00:00:00 878s Split 1, merged 1; iterating... 878s Splitting and merging 878s Splitting and merging time: 00:00:00 878s Split 1, merged 1; iterating... 878s Splitting and merging 878s Splitting and merging time: 00:00:00 878s Avg bucket size: 8.375 (target: 13) 878s Converting suffix-array elements to index image 878s Allocating ftab, absorbFtab 878s Entering Ebwt loop 878s Getting block 1 of 8 878s Reserving size (14) for bucket 1 878s Calculating Z arrays for bucket 1 878s Entering block accumulator loop for bucket 1: 878s bucket 1: 10% 878s bucket 1: 20% 878s bucket 1: 30% 878s bucket 1: 40% 878s bucket 1: 50% 878s bucket 1: 60% 878s bucket 1: 70% 878s bucket 1: 80% 878s bucket 1: 90% 878s bucket 1: 100% 878s Sorting block of length 7 for bucket 1 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 8 for bucket 1 878s Getting block 2 of 8 878s Reserving size (14) for bucket 2 878s Calculating Z arrays for bucket 2 878s Entering block accumulator loop for bucket 2: 878s bucket 2: 10% 878s bucket 2: 20% 878s bucket 2: 30% 878s bucket 2: 40% 878s bucket 2: 50% 878s bucket 2: 60% 878s bucket 2: 70% 878s bucket 2: 80% 878s bucket 2: 90% 878s bucket 2: 100% 878s Sorting block of length 10 for bucket 2 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 11 for bucket 2 878s Getting block 3 of 8 878s Reserving size (14) for bucket 3 878s Calculating Z arrays for bucket 3 878s Entering block accumulator loop for bucket 3: 878s bucket 3: 10% 878s bucket 3: 20% 878s bucket 3: 30% 878s bucket 3: 40% 878s bucket 3: 50% 878s bucket 3: 60% 878s bucket 3: 70% 878s bucket 3: 80% 878s bucket 3: 90% 878s bucket 3: 100% 878s Sorting block of length 13 for bucket 3 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 14 for bucket 3 878s Getting block 4 of 8 878s Reserving size (14) for bucket 4 878s Calculating Z arrays for bucket 4 878s Entering block accumulator loop for bucket 4: 878s bucket 4: 10% 878s bucket 4: 20% 878s bucket 4: 30% 878s bucket 4: 40% 878s bucket 4: 50% 878s bucket 4: 60% 878s bucket 4: 70% 878s bucket 4: 80% 878s bucket 4: 90% 878s bucket 4: 100% 878s Sorting block of length 5 for bucket 4 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 6 for bucket 4 878s Getting block 5 of 8 878s Reserving size (14) for bucket 5 878s Calculating Z arrays for bucket 5 878s Entering block accumulator loop for bucket 5: 878s bucket 5: 10% 878s bucket 5: 20% 878s bucket 5: 30% 878s bucket 5: 40% 878s bucket 5: 50% 878s bucket 5: 60% 878s bucket 5: 70% 878s bucket 5: 80% 878s bucket 5: 90% 878s bucket 5: 100% 878s Sorting block of length 13 for bucket 5 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 14 for bucket 5 878s Getting block 6 of 8 878s Reserving size (14) for bucket 6 878s Calculating Z arrays for bucket 6 878s Entering block accumulator loop for bucket 6: 878s bucket 6: 10% 878s bucket 6: 20% 878s bucket 6: 30% 878s bucket 6: 40% 878s bucket 6: 50% 878s bucket 6: 60% 878s bucket 6: 70% 878s bucket 6: 80% 878s bucket 6: 90% 878s bucket 6: 100% 878s Sorting block of length 2 for bucket 6 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 3 for bucket 6 878s Getting block 7 of 8 878s Reserving size (14) for bucket 7 878s Calculating Z arrays for bucket 7 878s Entering block accumulator loop for bucket 7: 878s bucket 7: 10% 878s bucket 7: 20% 878s bucket 7: 30% 878s bucket 7: 40% 878s bucket 7: 50% 878s bucket 7: 60% 878s bucket 7: 70% 878s bucket 7: 80% 878s bucket 7: 90% 878s bucket 7: 100% 878s Sorting block of length 13 for bucket 7 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 14 for bucket 7 878s Getting block 8 of 8 878s Reserving size (14) for bucket 8 878s Calculating Z arrays for bucket 8 878s Entering block accumulator loop for bucket 8: 878s bucket 8: 10% 878s bucket 8: 20% 878s bucket 8: 30% 878s bucket 8: 40% 878s bucket 8: 50% 878s bucket 8: 60% 878s bucket 8: 70% 878s bucket 8: 80% 878s bucket 8: 90% 878s bucket 8: 100% 878s Sorting block of length 4 for bucket 8 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 5 for bucket 8 878s Exited Ebwt loop 878s fchr[A]: 0 878s fchr[C]: 23 878s fchr[G]: 38 878s fchr[T]: 61 878s fchr[$]: 74 878s Exiting Ebwt::buildToDisk() 878s Returning from initFromVector 878s Wrote 4194563 bytes to primary EBWT file: /tmp/Sim.pm.77cQkkTL.1.bt2.tmp 878s Wrote 8 bytes to secondary EBWT file: /tmp/Sim.pm.77cQkkTL.2.bt2.tmp 878s Re-opening _in1 and _in2 as input streams 878s Returning from Ebwt constructor 878s Headers: 878s len: 74 878s bwtLen: 75 878s sz: 19 878s bwtSz: 19 878s lineRate: 6 878s offRate: 7 878s offMask: 0xffffff80 878s ftabChars: 10 878s eftabLen: 20 878s eftabSz: 80 878s ftabLen: 1048577 878s ftabSz: 4194308 878s offsLen: 1 878s offsSz: 4 878s lineSz: 64 878s sideSz: 64 878s sideBwtSz: 48 878s sideBwtLen: 192 878s numSides: 1 878s numLines: 1 878s ebwtTotLen: 64 878s ebwtTotSz: 64 878s color: 0 878s reverse: 0 878s Total time for call to driver() for forward index: 00:00:00 878s Reading reference sizes 878s Time reading reference sizes: 00:00:00 878s Calculating joined length 878s Writing header 878s Reserving space for joined string 878s Joining reference sequences 878s Time to join reference sequences: 00:00:00 878s Time to reverse reference sequence: 00:00:00 878s bmax according to bmaxDivN setting: 18 878s Using parameters --bmax 14 --dcv 1024 878s Doing ahead-of-time memory usage test 878s Passed! Constructing with these parameters: --bmax 14 --dcv 1024 878s Constructing suffix-array element generator 878s Building DifferenceCoverSample 878s Building sPrime 878s Building sPrimeOrder 878s V-Sorting samples 878s V-Sorting samples time: 00:00:00 878s Allocating rank array 878s Ranking v-sort output 878s Ranking v-sort output time: 00:00:00 878s Invoking Larsson-Sadakane on ranks 878s Invoking Larsson-Sadakane on ranks time: 00:00:00 878s Sanity-checking and returning 878s Building samples 878s Reserving space for 12 sample suffixes 878s Generating random suffixes 878s QSorting 12 sample offsets, eliminating duplicates 878s QSorting sample offsets, eliminating duplicates time: 00:00:00 878s Multikey QSorting 9 samples 878s (Using difference cover) 878s Multikey QSorting samples time: 00:00:00 878s Calculating bucket sizes 878s Splitting and merging 878s Splitting and merging time: 00:00:00 878s Avg bucket size: 7.33333 (target: 13) 878s Converting suffix-array elements to index image 878s Allocating ftab, absorbFtab 878s Entering Ebwt loop 878s Getting block 1 of 9 878s Reserving size (14) for bucket 1 878s Calculating Z arrays for bucket 1 878s Entering block accumulator loop for bucket 1: 878s bucket 1: 10% 878s bucket 1: 20% 878s bucket 1: 30% 878s bucket 1: 40% 878s bucket 1: 50% 878s bucket 1: 60% 878s bucket 1: 70% 878s bucket 1: 80% 878s bucket 1: 90% 878s bucket 1: 100% 878s Sorting block of length 3 for bucket 1 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 4 for bucket 1 878s Getting block 2 of 9 878s Reserving size (14) for bucket 2 878s Calculating Z arrays for bucket 2 878s Entering block accumulator loop for bucket 2: 878s bucket 2: 10% 878s bucket 2: 20% 878s bucket 2: 30% 878s bucket 2: 40% 878s bucket 2: 50% 878s bucket 2: 60% 878s bucket 2: 70% 878s bucket 2: 80% 878s bucket 2: 90% 878s bucket 2: 100% 878s Sorting block of length 10 for bucket 2 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 11 for bucket 2 878s Getting block 3 of 9 878s Reserving size (14) for bucket 3 878s Calculating Z arrays for bucket 3 878s Entering block accumulator loop for bucket 3: 878s bucket 3: 10% 878s bucket 3: 20% 878s bucket 3: 30% 878s bucket 3: 40% 878s bucket 3: 50% 878s bucket 3: 60% 878s bucket 3: 70% 878s bucket 3: 80% 878s bucket 3: 90% 878s bucket 3: 100% 878s Sorting block of length 8 for bucket 3 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 9 for bucket 3 878s Getting block 4 of 9 878s Reserving size (14) for bucket 4 878s Calculating Z arrays for bucket 4 878s Entering block accumulator loop for bucket 4: 878s bucket 4: 10% 878s bucket 4: 20% 878s bucket 4: 30% 878s bucket 4: 40% 878s bucket 4: 50% 878s bucket 4: 60% 878s bucket 4: 70% 878s bucket 4: 80% 878s bucket 4: 90% 878s bucket 4: 100% 878s Sorting block of length 13 for bucket 4 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 14 for bucket 4 878s Getting block 5 of 9 878s Reserving size (14) for bucket 5 878s Calculating Z arrays for bucket 5 878s Entering block accumulator loop for bucket 5: 878s bucket 5: 10% 878s bucket 5: 20% 878s bucket 5: 30% 878s bucket 5: 40% 878s bucket 5: 50% 878s bucket 5: 60% 878s bucket 5: 70% 878s bucket 5: 80% 878s bucket 5: 90% 878s bucket 5: 100% 878s Sorting block of length 6 for bucket 5 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 7 for bucket 5 878s Getting block 6 of 9 878s Reserving size (14) for bucket 6 878s Calculating Z arrays for bucket 6 878s Entering block accumulator loop for bucket 6: 878s bucket 6: 10% 878s bucket 6: 20% 878s bucket 6: 30% 878s bucket 6: 40% 878s bucket 6: 50% 878s bucket 6: 60% 878s bucket 6: 70% 878s bucket 6: 80% 878s bucket 6: 90% 878s bucket 6: 100% 878s Sorting block of length 11 for bucket 6 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 12 for bucket 6 878s Getting block 7 of 9 878s Reserving size (14) for bucket 7 878s Calculating Z arrays for bucket 7 878s Entering block accumulator loop for bucket 7: 878s bucket 7: 10% 878s bucket 7: 20% 878s bucket 7: 30% 878s bucket 7: 40% 878s bucket 7: 50% 878s bucket 7: 60% 878s bucket 7: 70% 878s bucket 7: 80% 878s bucket 7: 90% 878s bucket 7: 100% 878s Sorting block of length 2 for bucket 7 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 3 for bucket 7 878s Getting block 8 of 9 878s Reserving size (14) for bucket 8 878s Calculating Z arrays for bucket 8 878s Entering block accumulator loop for bucket 8: 878s bucket 8: 10% 878s bucket 8: 20% 878s bucket 8: 30% 878s bucket 8: 40% 878s bucket 8: 50% 878s bucket 8: 60% 878s bucket 8: 70% 878s bucket 8: 80% 878s bucket 8: 90% 878s bucket 8: 100% 878s Sorting block of length 12 for bucket 8 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 13 for bucket 8 878s Getting block 9 of 9 878s Reserving size (14) for bucket 9 878s Calculating Z arrays for bucket 9 878s Entering block accumulator loop for bucket 9: 878s bucket 9: 10% 878s bucket 9: 20% 878s bucket 9: 30% 878s bucket 9: 40% 878s bucket 9: 50% 878s bucket 9: 60% 878s bucket 9: 70% 878s bucket 9: 80% 878s bucket 9: 90% 878s bucket 9: 100% 878s Sorting block of length 1 for bucket 9 878s (Using difference cover) 878s Sorting block time: 00:00:00 878s Returning block of 2 for bucket 9 878s Exited Ebwt loop 878s fchr[A]: 0 878s fchr[C]: 23 878s fchr[G]: 38 878s fchr[T]: 61 878s fchr[$]: 74 878s Exiting Ebwt::buildToDisk() 878s Returning from initFromVector 878s Wrote 4194563 bytes to primary EBWT file: /tmp/Sim.pm.77cQkkTL.rev.1.bt2.tmp 878s Wrote 8 bytes to secondary EBWT file: /tmp/Sim.pm.77cQkkTL.rev.2.bt2.tmp 878s Re-opening _in1 and _in2 as input streams 878s Returning from Ebwt constructor 878s Headers: 878s Renaming /tmp/Sim.pm.77cQkkTL.3.bt2.tmp to /tmp/Sim.pm.77cQkkTL.3.bt2 878s Renaming /tmp/Sim.pm.77cQkkTL.4.bt2.tmp to /tmp/Sim.pm.77cQkkTL.4.bt2 878s Renaming /tmp/Sim.pm.77cQkkTL.1.bt2.tmp to /tmp/Sim.pm.77cQkkTL.1.bt2 878s Renaming /tmp/Sim.pm.77cQkkTL.2.bt2.tmp to /tmp/Sim.pm.77cQkkTL.2.bt2 878s Renaming /tmp/Sim.pm.77cQkkTL.rev.1.bt2.tmp to /tmp/Sim.pm.77cQkkTL.rev.1.bt2 878s Renaming /tmp/Sim.pm.77cQkkTL.rev.2.bt2.tmp to /tmp/Sim.pm.77cQkkTL.rev.2.bt2 878s Built nucleotide index '/tmp/Sim.pm.77cQkkTL' 878s Flattened IUPAC characters 878s Mutating sequence Sim.pm.1 878s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 878s Finished SNPs 878s Finished ref gaps 878s Finished read gaps 878s Mutating sequence Sim.pm.2 878s Introducing 14 SNPs, 0/1 ref/read gaps, and 0 rearrangements 878s Finished SNPs 878s Finished ref gaps 878s Finished read gaps 878s Mutated reference genome to subject genome 878s SNPs introduced: 14 878s Reference gaps introduced: 0 878s Read gaps introduced: 2 878s Rearrangements introduced: 0 878s Created read sampler 878s Sampling 114 reads 878s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 878s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 878s parsing sequence Sim.pm.1... 878s parsing sequence Sim.pm.2... 878s Parsed 74 reference bases 878s len: 74 878s bwtLen: 75 878s sz: 19 878s bwtSz: 19 878s lineRate: 6 878s offRate: 7 878s offMask: 0xffffff80 878s ftabChars: 10 878s eftabLen: 20 878s eftabSz: 80 878s ftabLen: 1048577 878s ftabSz: 4194308 878s offsLen: 1 878s offsSz: 4 878s lineSz: 64 878s sideSz: 64 878s sideBwtSz: 48 878s sideBwtLen: 192 878s numSides: 1 878s numLines: 1 878s ebwtTotLen: 64 878s ebwtTotSz: 64 878s color: 0 878s reverse: 1 878s Total time for backward call to driver() for mirror index: 00:00:00 878s *** Run 1 of 100 878s /usr/bin/bowtie2 --trim5 1 --rfg 15.4283113705024 --score-min L,4.75297795655352,6.55463133898734 --np 2 -R 4 --trim3 0 --mp 9.17359867121833,6.3979569956783 --rdg 18.2749548341945,4.16183678841038 --local --cp-min 2 --cp-ival 1 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 879s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 879s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 879s Warning: skipping mate #1 of read '4' because it was < 2 characters long 879s Warning: skipping mate #2 of read '4' because it was < 2 characters long 879s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 879s Warning: skipping mate #2 of read '8' because it was < 2 characters long 879s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 879s Warning: skipping mate #1 of read '28' because it was < 2 characters long 879s Read 50 alignments... 879s Warning: skipping mate #2 of read '79' because length (1) <= # seed mismatches (0) 879s Warning: skipping mate #2 of read '79' because it was < 2 characters long 879s Read 100 alignments... 879s Read 150 alignments... 879s 114 reads; of these: 879s 113 (99.12%) were paired; of these: 879s 113 (100.00%) aligned concordantly 0 times 879s 0 (0.00%) aligned concordantly exactly 1 time 879s 0 (0.00%) aligned concordantly >1 times 879s ---- 879s 113 pairs aligned concordantly 0 times; of these: 879s 0 (0.00%) aligned discordantly 1 time 879s ---- 879s 113 pairs aligned 0 times concordantly or discordantly; of these: 879s 226 mates make up the pairs; of these: 879s 226 (100.00%) aligned 0 times 879s 0 (0.00%) aligned exactly 1 time 879s 0 (0.00%) aligned >1 times 879s 1 (0.88%) were unpaired; of these: 879s 1 (100.00%) aligned 0 times 879s 0 (0.00%) aligned exactly 1 time 879s 0 (0.00%) aligned >1 times 879s 0.00% overall alignment rate 879s Read 200 alignments... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s /usr/bin/bowtie2 --trim5 1 --rfg 15.4283113705024 --score-min L,4.75297795655352,6.55463133898734 --np 2 -R 4 --trim3 0 --mp 9.17359867121833,6.3979569956783 --rdg 18.2749548341945,4.16183678841038 --local --cp-min 2 --cp-ival 1 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s Processing line... 879s --- Summary --- 879s Read 1 reference strings 879s Checked 0 alignments, 0 edits 879s --------------- 879s PASSED 879s ALSO checking that bowtie2 and bowtie2-align match up 879s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 879s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 879s Warning: skipping mate #1 of read '4' because it was < 2 characters long 879s Warning: skipping mate #2 of read '4' because it was < 2 characters long 879s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 879s Warning: skipping mate #2 of read '8' because it was < 2 characters long 879s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 879s Warning: skipping mate #1 of read '28' because it was < 2 characters long 879s Warning: skipping mate #2 of read '79' because length (1) <= # seed mismatches (0) 879s Warning: skipping mate #2 of read '79' because it was < 2 characters long 879s 114 reads; of these: 879s 113 (99.12%) were paired; of these: 879s 113 (100.00%) aligned concordantly 0 times 879s 0 (0.00%) aligned concordantly exactly 1 time 879s 0 (0.00%) aligned concordantly >1 times 879s ---- 879s 113 pairs aligned concordantly 0 times; of these: 879s 0 (0.00%) aligned discordantly 1 time 879s ---- 879s 113 pairs aligned 0 times concordantly or discordantly; of these: 879s 226 mates make up the pairs; of these: 879s 226 (100.00%) aligned 0 times 879s 0 (0.00%) aligned exactly 1 time 879s 0 (0.00%) aligned >1 times 879s 1 (0.88%) were unpaired; of these: 879s 1 (100.00%) aligned 0 times 879s 0 (0.00%) aligned exactly 1 time 879s 0 (0.00%) aligned >1 times 879s 0.00% overall alignment rate 879s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 879s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 879s /usr/bin/bowtie2 --trim5 1 --rfg 15.4283113705024 --score-min L,4.75297795655352,6.55463133898734 --np 2 -R 4 --trim3 0 --mp 9.17359867121833,6.3979569956783 --rdg 18.2749548341945,4.16183678841038 --local --cp-min 2 --cp-ival 1 -q -p 4 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 879s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 879s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 879s Warning: skipping mate #1 of read '4' because it was < 2 characters long 879s Warning: skipping mate #2 of read '4' because it was < 2 characters long 879s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 879s Warning: skipping mate #2 of read '8' because it was < 2 characters long 879s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 879s Warning: skipping mate #1 of read '28' because it was < 2 characters long 879s Warning: skipping mate #2 of read '79' because length (1) <= # seed mismatches (0) 879s Warning: skipping mate #2 of read '79' because it was < 2 characters long 879s 114 reads; of these: 879s 113 (99.12%) were paired; of these: 879s 113 (100.00%) aligned concordantly 0 times 879s 0 (0.00%) aligned concordantly exactly 1 time 879s 0 (0.00%) aligned concordantly >1 times 879s ---- 879s 113 pairs aligned concordantly 0 times; of these: 879s 0 (0.00%) aligned discordantly 1 time 879s ---- 879s 113 pairs aligned 0 times concordantly or discordantly; of these: 879s 226 mates make up the pairs; of these: 879s 226 (100.00%) aligned 0 times 879s 0 (0.00%) aligned exactly 1 time 879s 0 (0.00%) aligned >1 times 879s 1 (0.88%) were unpaired; of these: 879s 1 (100.00%) aligned 0 times 879s 0 (0.00%) aligned exactly 1 time 879s 0 (0.00%) aligned >1 times 879s 0.00% overall alignment rate 879s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 879s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 879s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 879s Flattened IUPAC characters 879s Mutating sequence Sim.pm.1 879s Introducing 3 SNPs, 2/1 ref/read gaps, and 1 rearrangements 879s Finished SNPs 879s Finished ref gaps 879s Finished read gaps 879s Mutating sequence Sim.pm.2 879s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 879s Finished SNPs 879s Finished ref gaps 879s Finished read gaps 879s Mutated reference genome to subject genome 879s SNPs introduced: 3 879s Reference gaps introduced: 3 879s Read gaps introduced: 1 879s Rearrangements introduced: 1 879s Created read sampler 879s Sampling 23 reads 879s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 879s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 879s parsing sequence Sim.pm.1... 879s parsing sequence Sim.pm.2... 879s Parsed 74 reference bases 879s *** Run 2 of 100 879s /usr/bin/bowtie2 --rdg 7.26116018006514 --ma 19.4951208602103 -M 4 --cp-min 6 --cp-ival 1 --mm --trim5 1 -i C,4.90269382331938 --rfg 2.65177058447176,18.2236976735361 --n-ceil 0.66133032143725,1.49183635846995 --score-min L,2.40003171423576,7.79736229254669 --np 5 --norc --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq 880s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 880s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s 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 880s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 880s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 880s 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 880s 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 880s 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 880s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 880s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 880s 23 reads; of these: 880s 23 (100.00%) were unpaired; of these: 880s 23 (100.00%) aligned 0 times 880s 0 (0.00%) aligned exactly 1 time 880s 0 (0.00%) aligned >1 times 880s 0.00% overall alignment rate 880s *** Run 3 of 100 880s /usr/bin/bowtie2 --trim3 1 --mp 9.97001165731391,4.01049587265223 -k 3 --score-min L,1.71645710333197,8.99582822930319 --cp-min 3 --norc --cp-ival 1 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s --- Summary --- 880s Read 1 reference strings 880s Checked 0 alignments, 0 edits 880s --------------- 880s PASSED 880s Flattened IUPAC characters 880s Mutating sequence Sim.pm.2 880s Introducing 1 SNPs, 1/2 ref/read gaps, and 1 rearrangements 880s Finished SNPs 880s Finished ref gaps 880s Finished read gaps 880s Mutating sequence Sim.pm.1 880s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 880s Finished SNPs 880s Finished ref gaps 880s Finished read gaps 880s Mutated reference genome to subject genome 880s SNPs introduced: 1 880s Reference gaps introduced: 1 880s Read gaps introduced: 2 880s Rearrangements introduced: 1 880s Created read sampler 880s Sampling 46 reads 880s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 880s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 880s parsing sequence Sim.pm.1... 880s parsing sequence Sim.pm.2... 880s Parsed 74 reference bases 880s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 880s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 880s Warning: skipping read '6' because it was < 2 characters long 880s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 880s 46 reads; of these: 880s /usr/bin/bowtie2 --trim3 1 --mp 9.97001165731391,4.01049587265223 -k 3 --score-min L,1.71645710333197,8.99582822930319 --cp-min 3 --norc --cp-ival 1 -q -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 880s 46 (100.00%) were unpaired; of these: 880s 40 (86.96%) aligned 0 times 880s 3 (6.52%) aligned exactly 1 time 880s 3 (6.52%) aligned >1 times 880s 13.04% overall alignment rate 880s Read 50 alignments... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s TC 880s TC 880s Processing line... 880s TC 880s TC 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s AA 880s AA 880s Processing line... 880s AA 880s AA 880s Processing line... 880s AA 880s AA 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s GGAGGGCGATA 880s GGAGGGCGATA 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s TGTACATGACTCT 880s TGTACATGACTCT 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s ACAAAGAGG 880s ACAAAGAGG 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s CT 880s CT 880s Processing line... 880s CT 880s CT 880s Processing line... 880s CT 880s CT 880s --- Summary --- 880s Read 1 reference strings 880s Checked 11 alignments, 0 edits 880s --------------- 880s PASSED 880s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 880s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 880s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 880s Warning: skipping read '6' because it was < 2 characters long 880s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 880s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 880s 46 reads; of these: 880s 46 (100.00%) were unpaired; of these: 880s 40 (86.96%) aligned 0 times 880s 3 (6.52%) aligned exactly 1 time 880s 3 (6.52%) aligned >1 times 880s 13.04% overall alignment rate 880s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 880s Flattened IUPAC characters 880s Mutating sequence Sim.pm.1 880s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 880s Finished SNPs 880s Finished ref gaps 880s Finished read gaps 880s Mutating sequence Sim.pm.2 880s Introducing 11 SNPs, 0/0 ref/read gaps, and 2 rearrangements 880s Finished SNPs 880s Finished ref gaps 880s Finished read gaps 880s Mutated reference genome to subject genome 880s SNPs introduced: 12 880s Reference gaps introduced: 1 880s Read gaps introduced: 0 880s Rearrangements introduced: 2 880s Created read sampler 880s Sampling 18 reads 880s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 880s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 880s parsing sequence Sim.pm.1... 880s parsing sequence Sim.pm.2... 880s Parsed 74 reference bases 880s *** Run 4 of 100 880s /usr/bin/bowtie2 --nofw --n-ceil 0.14038001090861,0.331128261585674 --score-min L,4.20558665062993,4.32479387270635 --trim5 7 --rfg 18.1891186582274 --mm --cp-ival 1 --cp-min 4 --mp 6.70521276348414,5.95471555979495 --trim3 8 --local -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 880s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '4' because it was < 2 characters long 880s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '9' because it was < 2 characters long 880s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '11' because it was < 2 characters long 880s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '12' because it was < 2 characters long 880s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '13' because it was < 2 characters long 880s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '15' because it was < 2 characters long 880s 18 reads; of these: 880s 18 (100.00%) were unpaired; of these: 880s 18 (100.00%) aligned 0 times 880s 0 (0.00%) aligned exactly 1 time 880s 0 (0.00%) aligned >1 times 880s 0.00% overall alignment rate 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s Processing line... 880s --- Summary --- 880s Read 1 reference strings 880s Checked 0 alignments, 0 edits 880s --------------- 880s PASSED 880s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 880s /usr/bin/bowtie2 --nofw --n-ceil 0.14038001090861,0.331128261585674 --score-min L,4.20558665062993,4.32479387270635 --trim5 7 --rfg 18.1891186582274 --mm --cp-ival 1 --cp-min 4 --mp 6.70521276348414,5.95471555979495 --trim3 8 --local -q -p 2 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 880s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '4' because it was < 2 characters long 880s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '9' because it was < 2 characters long 880s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '11' because it was < 2 characters long 880s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '12' because it was < 2 characters long 880s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '13' because it was < 2 characters long 880s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 880s Warning: skipping read '15' because it was < 2 characters long 880s 18 reads; of these: 880s 18 (100.00%) were unpaired; of these: 880s 18 (100.00%) aligned 0 times 880s 0 (0.00%) aligned exactly 1 time 880s 0 (0.00%) aligned >1 times 880s 0.00% overall alignment rate 880s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 880s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 880s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 880s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 880s /usr/bin/bowtie2 --nofw --n-ceil 0.14038001090861,0.331128261585674 --score-min L,4.20558665062993,4.32479387270635 --trim5 7 --rfg 18.1891186582274 --mm --cp-ival 1 --cp-min 4 --mp 6.70521276348414,5.95471555979495 --trim3 8 --local -q -p 3 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 881s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 881s Warning: skipping read '4' because it was < 2 characters long 881s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 881s Warning: skipping read '9' because it was < 2 characters long 881s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 881s Warning: skipping read '11' because it was < 2 characters long 881s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 881s Warning: skipping read '12' because it was < 2 characters long 881s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 881s Warning: skipping read '13' because it was < 2 characters long 881s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 881s Warning: skipping read '15' because it was < 2 characters long 881s 18 reads; of these: 881s 18 (100.00%) were unpaired; of these: 881s 18 (100.00%) aligned 0 times 881s 0 (0.00%) aligned exactly 1 time 881s 0 (0.00%) aligned >1 times 881s 0.00% overall alignment rate 881s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 881s Flattened IUPAC characters 881s Mutating sequence Sim.pm.2 881s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 881s Finished SNPs 881s Finished ref gaps 881s Finished read gaps 881s Mutating sequence Sim.pm.1 881s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 881s Finished SNPs 881s Finished ref gaps 881s Finished read gaps 881s Mutated reference genome to subject genome 881s SNPs introduced: 5 881s Reference gaps introduced: 1 881s Read gaps introduced: 2 881s Rearrangements introduced: 0 881s Created read sampler 881s Sampling 58 reads 881s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 881s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 881s parsing sequence Sim.pm.1... 881s parsing sequence Sim.pm.2... 881s Parsed 74 reference bases 881s *** Run 5 of 100 881s /usr/bin/bowtie2 --cp-min 8 --mm --cp-ival 1 --rdg 23.783536542021,5.95972788081359 --local --norc --np 3 -D 30 --rfg 27.395714245567,17.2162164707568 --gbar 5 --score-min L,7.31000922031272,5.70944776539833 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 881s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 881s Warning: skipping mate #2 of read '36' because it was < 2 characters long 881s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 881s Warning: skipping mate #1 of read '48' because it was < 2 characters long 881s 58 reads; of these: 881s 58 (100.00%) were paired; of these: 881s 58 (100.00%) aligned concordantly 0 times 881s 0 (0.00%) aligned concordantly exactly 1 time 881s 0 (0.00%) aligned concordantly >1 times 881s ---- 881s 58 pairs aligned concordantly 0 times; of these: 881s 0 (0.00%) aligned discordantly 1 time 881s ---- 881s 58 pairs aligned 0 times concordantly or discordantly; of these: 881s 116 mates make up the pairs; of these: 881s 116 (100.00%) aligned 0 times 881s 0 (0.00%) aligned exactly 1 time 881s 0 (0.00%) aligned >1 times 881s 0.00% overall alignment rate 881s Read 50 alignments... 881s Read 100 alignments... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s --- Summary --- 881s Read 1 reference strings 881s Checked 0 alignments, 0 edits 881s --------------- 881s PASSED 881s Flattened IUPAC characters 881s Mutating sequence Sim.pm.1 881s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 881s Finished SNPs 881s Finished ref gaps 881s Finished read gaps 881s Mutating sequence Sim.pm.2 881s Introducing 5 SNPs, 0/0 ref/read gaps, and 3 rearrangements 881s Finished SNPs 881s Finished ref gaps 881s Finished read gaps 881s Mutated reference genome to subject genome 881s SNPs introduced: 12 881s Reference gaps introduced: 1 881s Read gaps introduced: 0 881s Rearrangements introduced: 3 881s Created read sampler 881s Sampling 51 reads 881s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 881s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 881s parsing sequence Sim.pm.1... 881s parsing sequence Sim.pm.2... 881s Parsed 74 reference bases 881s *** Run 6 of 100 881s /usr/bin/bowtie2 --norc --rfg 36.222215577908,13.787246741781 --score-min L,1.10115553140557,2.37040034843796 --cp-min 3 --cp-ival 4 --local --trim3 8 --mp 8.67527655390953,8.34743433656726 -a --rdg 17.6024341444517 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 881s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 881s Warning: skipping mate #1 of read '2' because it was < 2 characters long 881s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 881s Warning: skipping mate #1 of read '4' because it was < 2 characters long 881s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 881s Warning: skipping read '11' because it was < 2 characters long 881s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 881s Warning: skipping mate #1 of read '18' because it was < 2 characters long 881s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 881s Warning: skipping mate #1 of read '25' because it was < 2 characters long 881s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 881s Warning: skipping read '26' because it was < 2 characters long 881s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 881s Warning: skipping mate #1 of read '27' because it was < 2 characters long 881s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 881s Warning: skipping mate #1 of read '33' because it was < 2 characters long 881s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 881s Warning: skipping mate #1 of read '39' because it was < 2 characters long 881s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 881s Warning: skipping mate #1 of read '44' because it was < 2 characters long 881s 51 reads; of these: 881s 39 (76.47%) were paired; of these: 881s 39 (100.00%) aligned concordantly 0 times 881s 0 (0.00%) aligned concordantly exactly 1 time 881s 0 (0.00%) aligned concordantly >1 times 881s ---- 881s 39 pairs aligned concordantly 0 times; of these: 881s 0 (0.00%) aligned discordantly 1 time 881s ---- 881s 39 pairs aligned 0 times concordantly or discordantly; of these: 881s 78 mates make up the pairs; of these: 881s 78 (100.00%) aligned 0 times 881s 0 (0.00%) aligned exactly 1 time 881s 0 (0.00%) aligned >1 times 881s 12 (23.53%) were unpaired; of these: 881s 12 (100.00%) aligned 0 times 881s 0 (0.00%) aligned exactly 1 time 881s 0 (0.00%) aligned >1 times 881s 0.00% overall alignment rate 881s Read 50 alignments... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s --- Summary --- 881s Read 1 reference strings 881s Checked 0 alignments, 0 edits 881s --------------- 881s PASSED 881s Flattened IUPAC characters 881s Mutating sequence Sim.pm.1 881s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 881s Finished SNPs 881s Finished ref gaps 881s Finished read gaps 881s Mutating sequence Sim.pm.2 881s Introducing 0 SNPs, 1/1 ref/read gaps, and 1 rearrangements 881s Finished SNPs 881s Finished ref gaps 881s Finished read gaps 881s Mutated reference genome to subject genome 881s SNPs introduced: 4 881s Reference gaps introduced: 1 881s Read gaps introduced: 1 881s Rearrangements introduced: 2 881s Created read sampler 881s Sampling 66 reads 881s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 881s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 881s parsing sequence Sim.pm.1... 881s parsing sequence Sim.pm.2... 881s Parsed 74 reference bases 881s *** Run 7 of 100 881s /usr/bin/bowtie2 --nofw --n-ceil 1.37808170571781,0.538161521192514 --score-min L,9.92592768124484,4.68237981945383 --cp-ival 1 --cp-min 4 --rdg 2.20362969688537,18.6257167827272 -a --mp 4.04776824454791,2.26529184009405 --local -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 881s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 881s Warning: skipping read '8' because it was < 2 characters long 881s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 881s Warning: skipping read '10' because it was < 2 characters long 881s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 881s Warning: skipping read '14' because it was < 2 characters long 881s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 881s Warning: skipping read '53' because it was < 2 characters long 881s 66 reads; of these: 881s 66 (100.00%) were unpaired; of these: 881s 66 (100.00%) aligned 0 times 881s 0 (0.00%) aligned exactly 1 time 881s 0 (0.00%) aligned >1 times 881s 0.00% overall alignment rate 881s Read 50 alignments... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s /usr/bin/bowtie2 --nofw --n-ceil 1.37808170571781,0.538161521192514 --score-min L,9.92592768124484,4.68237981945383 --cp-ival 1 --cp-min 4 --rdg 2.20362969688537,18.6257167827272 -a --mp 4.04776824454791,2.26529184009405 --local -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s Processing line... 881s --- Summary --- 881s Read 1 reference strings 881s Checked 0 alignments, 0 edits 881s --------------- 881s PASSED 881s ALSO checking that bowtie2 and bowtie2-align match up 882s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 882s Warning: skipping read '8' because it was < 2 characters long 882s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 882s Warning: skipping read '10' because it was < 2 characters long 882s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 882s Warning: skipping read '14' because it was < 2 characters long 882s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 882s Warning: skipping read '53' because it was < 2 characters long 882s 66 reads; of these: 882s 66 (100.00%) were unpaired; of these: 882s 66 (100.00%) aligned 0 times 882s 0 (0.00%) aligned exactly 1 time 882s 0 (0.00%) aligned >1 times 882s 0.00% overall alignment rate 882s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 882s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 882s /usr/bin/bowtie2 --nofw --n-ceil 1.37808170571781,0.538161521192514 --score-min L,9.92592768124484,4.68237981945383 --cp-ival 1 --cp-min 4 --rdg 2.20362969688537,18.6257167827272 -a --mp 4.04776824454791,2.26529184009405 --local -q -p 3 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 882s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 882s Warning: skipping read '8' because it was < 2 characters long 882s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 882s Warning: skipping read '10' because it was < 2 characters long 882s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 882s Warning: skipping read '14' because it was < 2 characters long 882s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 882s Warning: skipping read '53' because it was < 2 characters long 882s 66 reads; of these: 882s 66 (100.00%) were unpaired; of these: 882s 66 (100.00%) aligned 0 times 882s 0 (0.00%) aligned exactly 1 time 882s 0 (0.00%) aligned >1 times 882s 0.00% overall alignment rate 882s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 882s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 882s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 882s Flattened IUPAC characters 882s Mutating sequence Sim.pm.2 882s Introducing 14 SNPs, 0/1 ref/read gaps, and 1 rearrangements 882s Finished SNPs 882s Finished ref gaps 882s Finished read gaps 882s Mutating sequence Sim.pm.1 882s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 882s Finished SNPs 882s Finished ref gaps 882s Finished read gaps 882s Mutated reference genome to subject genome 882s SNPs introduced: 20 882s Reference gaps introduced: 0 882s Read gaps introduced: 1 882s Rearrangements introduced: 1 882s Created read sampler 882s Sampling 76 reads 882s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 882s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 882s parsing sequence Sim.pm.1... 882s parsing sequence Sim.pm.2... 882s Parsed 74 reference bases 882s *** Run 8 of 100 882s /usr/bin/bowtie2 --cp-ival 2 -N 0 -L15 --np 3 --norc --cp-min 2 --score-min L,1.40821089208961,7.75639335033178 --n-ceil 0.523895084173923,0.994072582105254 --local --trim5 5 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq 882s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 882s 76 reads; of these: 882s 76 (100.00%) were unpaired; of these: 882s 76 (100.00%) aligned 0 times 882s 0 (0.00%) aligned exactly 1 time 882s 0 (0.00%) aligned >1 times 882s 0.00% overall alignment rate 882s Read 50 alignments... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s /usr/bin/bowtie2 --cp-ival 2 -N 0 -L15 --np 3 --norc --cp-min 2 --score-min L,1.40821089208961,7.75639335033178 --n-ceil 0.523895084173923,0.994072582105254 --local --trim5 5 --qseq -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s Processing line... 882s --- Summary --- 882s Read 1 reference strings 882s Checked 0 alignments, 0 edits 882s --------------- 882s PASSED 882s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 882s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 882s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 882s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 882s 76 reads; of these: 882s 76 (100.00%) were unpaired; of these: 882s 76 (100.00%) aligned 0 times 882s 0 (0.00%) aligned exactly 1 time 882s 0 (0.00%) aligned >1 times 882s 0.00% overall alignment rate 882s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 882s Flattened IUPAC characters 882s Mutating sequence Sim.pm.1 882s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 882s Finished SNPs 882s Finished ref gaps 882s Finished read gaps 882s Mutating sequence Sim.pm.2 882s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 882s Finished SNPs 882s Finished ref gaps 882s Finished read gaps 882s Mutated reference genome to subject genome 882s SNPs introduced: 5 882s Reference gaps introduced: 1 882s Read gaps introduced: 1 882s Rearrangements introduced: 0 882s Created read sampler 882s Sampling 65 reads 882s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 882s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 882s parsing sequence Sim.pm.1... 882s parsing sequence Sim.pm.2... 882s *** Run 9 of 100 882s /usr/bin/bowtie2 -N 0 -L28 --score-min L,7.9344110122998,4.03145792366654 -i S,1.56136298306093 --rfg 1.13560766518426 --trim5 4 --cp-ival 2 --cp-min 2 -M 2 --trim3 8 --mp 9.15082385755146,1.82164512660347 -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw 882s Parsed 74 reference bases 883s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 883s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '1' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 883s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '3' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 883s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '6' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 883s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '15' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 883s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '16' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 883s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '25' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 883s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '27' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 883s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '31' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 883s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '38' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 883s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '40' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 883s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 883s Warning: skipping read '47' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 883s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 883s Warning: skipping read '53' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 883s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '59' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 883s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 883s Warning: skipping read '63' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 883s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '64' because it was < 2 characters long 883s Read 50 alignments... 883s Read 100 alignments... 883s 65 reads; of these: 883s 51 (78.46%) were paired; of these: 883s 51 (100.00%) aligned concordantly 0 times 883s 0 (0.00%) aligned concordantly exactly 1 time 883s 0 (0.00%) aligned concordantly >1 times 883s ---- 883s 51 pairs aligned concordantly 0 times; of these: 883s 0 (0.00%) aligned discordantly 1 time 883s ---- 883s 51 pairs aligned 0 times concordantly or discordantly; of these: 883s 102 mates make up the pairs; of these: 883s 88 (86.27%) aligned 0 times 883s 11 (10.78%) aligned exactly 1 time 883s 3 (2.94%) aligned >1 times 883s 14 (21.54%) were unpaired; of these: 883s 9 (64.29%) aligned 0 times 883s 4 (28.57%) aligned exactly 1 time 883s 1 (7.14%) aligned >1 times 883s 16.38% overall alignment rate 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s AC 883s AC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s ATGA 883s ATGA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GG 883s GG 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s ACAAAGAGGCGGGGTAACATTC 883s ACAAAGAGGCGGGGTAACATTC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s ACTCTTTACACAAAGAGGCGGGGTA 883s ACTCTTTACACAAAGAGGCGGGGTA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GGGG 883s GGGG 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GAGGC 883s GAGGC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s TCTTTACAC 883s TCTTTACAC 883s Processing line... 883s GGG 883s GGG 883s Processing line... 883s Processing line... 883s GGTAACATTCAGCTACC 883s GGTAACATTCAGCTACC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s ACAAAGAGGCGGGGTAACATTC 883s ACAAAGAGGCGGGGTAACATTC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GACT 883s GACT 883s Processing line... 883s Processing line... 883s CTCTTTACA 883s CTCTTTACA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GGTGTACATGACTCTT 883s GGTGTACATGACTCTT 883s Processing line... 883s Processing line... 883s CA 883s CA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GTACAT 883s GTACAT 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GTACATGACTCTTTACACAAAGAGGCGGGGT 883s GTACATGACTCTTTACACAAAGAGGCGGGGT 883s Processing line... 883s Processing line... 883s ACAAAGAGGCGGG 883s ACAAAGAGGCGGG 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s AGAGGCGGGGTAACATTCAGCT 883s AGAGGCGGGGTAACATTCAGCT 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s --- Summary --- 883s Read 1 reference strings 883s Checked 19 alignments, 0 edits 883s --------------- 883s PASSED 883s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 883s /usr/bin/bowtie2 -N 0 -L28 --score-min L,7.9344110122998,4.03145792366654 -i S,1.56136298306093 --rfg 1.13560766518426 --trim5 4 --cp-ival 2 --cp-min 2 -M 2 --trim3 8 --mp 9.15082385755146,1.82164512660347 -r -p 3 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 883s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 883s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '1' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 883s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '3' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 883s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '16' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 883s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '6' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 883s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '15' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 883s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '38' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 883s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 883s Warning: skipping read '53' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 883s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '59' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 883s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 883s Warning: skipping read '63' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 883s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '64' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 883s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '25' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 883s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '40' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 883s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 883s Warning: skipping read '47' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 883s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '27' because it was < 2 characters long 883s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 883s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 883s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 883s Warning: skipping mate #1 of read '31' because it was < 2 characters long 883s 65 reads; of these: 883s 51 (78.46%) were paired; of these: 883s 51 (100.00%) aligned concordantly 0 times 883s 0 (0.00%) aligned concordantly exactly 1 time 883s 0 (0.00%) aligned concordantly >1 times 883s ---- 883s 51 pairs aligned concordantly 0 times; of these: 883s 0 (0.00%) aligned discordantly 1 time 883s ---- 883s 51 pairs aligned 0 times concordantly or discordantly; of these: 883s 102 mates make up the pairs; of these: 883s 88 (86.27%) aligned 0 times 883s 11 (10.78%) aligned exactly 1 time 883s 3 (2.94%) aligned >1 times 883s 14 (21.54%) were unpaired; of these: 883s 9 (64.29%) aligned 0 times 883s 4 (28.57%) aligned exactly 1 time 883s 1 (7.14%) aligned >1 times 883s 16.38% overall alignment rate 883s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 883s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 883s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 883s Flattened IUPAC characters 883s Mutating sequence Sim.pm.1 883s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 883s Finished SNPs 883s Finished ref gaps 883s Finished read gaps 883s Mutating sequence Sim.pm.2 883s Introducing 1 SNPs, 0/0 ref/read gaps, and 3 rearrangements 883s Finished SNPs 883s Finished ref gaps 883s Finished read gaps 883s Mutated reference genome to subject genome 883s SNPs introduced: 8 883s Reference gaps introduced: 0 883s Read gaps introduced: 0 883s Rearrangements introduced: 3 883s Created read sampler 883s Sampling 150 reads 883s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 883s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 883s parsing sequence Sim.pm.1... 883s parsing sequence Sim.pm.2... 883s Parsed 74 reference bases 883s *** Run 10 of 100 883s /usr/bin/bowtie2 -R 4 --cp-ival 2 --mm -N 1 -L13 --np 2 --cp-min 2 --score-min L,7.06375536621511,5.83731354827604 --ma 14.2451124297616 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq 883s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 883s 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 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 883s 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 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 883s 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 883s 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 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 883s 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 883s 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 883s 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 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 883s 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 883s 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 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (1) <= # seed mismatches (1) 883s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s 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 883s Read 50 alignments... 883s Read 100 alignments... 883s 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 883s 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 883s 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 883s 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 883s 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 883s 150 reads; of these: 883s 150 (100.00%) were unpaired; of these: 883s 116 (77.33%) aligned 0 times 883s 23 (15.33%) aligned exactly 1 time 883s 11 (7.33%) aligned >1 times 883s 22.67% overall alignment rate 883s Read 150 alignments... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GGAG 883s GGAG 883s Processing line... 883s Processing line... 883s Processing line... 883s GG 883s GG 883s Processing line... 883s Processing line... 883s GTGTACATGACTCTTTACACAAAGAGGCGGGGTAAC 883s GTGTACATGACTCTTTACACAAAGAGGCGGGGTAAC 883s Processing line... 883s CACAA 883s CACAA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s AGA 883s AGA 883s Processing line... 883s Processing line... 883s AT 883s AT 883s Processing line... 883s Processing line... 883s TTTACACAA 883s TTTACACAA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s ATGACTCTTTACAC 883s ATGACTCTTTACAC 883s Processing line... 883s TCA 883s TCA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s AACATT 883s AACATT 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s TGACTCTTTACACAAAGA 883s TGACTCTTTACACAAAGA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s AAA 883s AAA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s AA 883s AA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s TTT 883s TTT 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s CTTTACACAAAGAGGCGGGGTAACAT 883s CTTTACACAAAGAGGCGGGGTAACAT 883s Processing line... 883s ACAAAGAGGCG 883s ACAAAGAGGCG 883s Processing line... 883s TTC 883s TTC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s CATGACTCTTTACACAAAGAGGC 883s CATGACTCTTTACACAAAGAGGC 883s Processing line... 883s Processing line... 883s CTTTAC 883s CTTTAC 883s Processing line... 883s Processing line... 883s TACACAAA 883s TACACAAA 883s Processing line... 883s Processing line... 883s Processing line... 883s CATGACTCTTTACACAAAGA 883s CATGACTCTTTACACAAAGA 883s Processing line... 883s /usr/bin/bowtie2 -R 4 --cp-ival 2 --mm -N 1 -L13 --np 2 --cp-min 2 --score-min L,7.06375536621511,5.83731354827604 --ma 14.2451124297616 --qseq -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 883s GGA 883s GGA 883s Processing line... 883s CTCTTTACACAAAGAGGCGGGGTAACATTCAGCTACCA 883s CTCTTTACACAAAGAGGCGGGGTAACATTCAGCTACCA 883s Processing line... 883s Processing line... 883s AAGGGCC 883s AAGGGCC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s AAC 883s AAC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s ACTC 883s ACTC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GCTA 883s GCTA 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GCGATA 883s GCGATA 883s Processing line... 883s Processing line... 883s TAAC 883s TAAC 883s Processing line... 883s ATGACTCTTTACAC 883s ATGACTCTTTACAC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s ACATGACTCTTTACACAAAG 883s ACATGACTCTTTACACAAAG 883s Processing line... 883s GCG 883s GCG 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GAT 883s GAT 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s GC 883s GC 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s Processing line... 883s --- Summary --- 883s Read 1 reference strings 883s Checked 34 alignments, 0 edits 883s --------------- 883s PASSED 883s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 884s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 884s 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 884s 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 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 884s 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 884s 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 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 884s 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 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 884s 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 884s 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 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (1) <= # seed mismatches (1) 884s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 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 884s 150 reads; of these: 884s 150 (100.00%) were unpaired; of these: 884s 116 (77.33%) aligned 0 times 884s 23 (15.33%) aligned exactly 1 time 884s 11 (7.33%) aligned >1 times 884s 22.67% overall alignment rate 884s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 884s Flattened IUPAC characters 884s Mutating sequence Sim.pm.1 884s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 884s Finished SNPs 884s Finished ref gaps 884s Finished read gaps 884s Mutating sequence Sim.pm.2 884s Introducing 13 SNPs, 0/2 ref/read gaps, and 1 rearrangements 884s Finished SNPs 884s Finished ref gaps 884s Finished read gaps 884s Mutated reference genome to subject genome 884s SNPs introduced: 13 884s Reference gaps introduced: 0 884s Read gaps introduced: 2 884s Rearrangements introduced: 1 884s Created read sampler 884s Sampling 55 reads 884s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 884s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 884s parsing sequence Sim.pm.1... 884s parsing sequence Sim.pm.2... 884s Parsed 74 reference bases 884s *** Run 11 of 100 884s /usr/bin/bowtie2 --n-ceil 0.91504050943928,1.27976118553416 --ma 20.9393668388232 --score-min L,8.40087606249119,5.14307786857785 -k 4 --rfg 48.0996965926486,6.61880515543671 -N 1 -L29 --mm --cp-ival 2 --cp-min 3 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 884s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 884s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (1) 884s Warning: skipping mate #1 of read '37' because it was < 2 characters long 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 884s 55 reads; of these: 884s 55 (100.00%) were paired; of these: 884s 54 (98.18%) aligned concordantly 0 times 884s 1 (1.82%) aligned concordantly exactly 1 time 884s 0 (0.00%) aligned concordantly >1 times 884s ---- 884s 54 pairs aligned concordantly 0 times; of these: 884s 0 (0.00%) aligned discordantly 1 time 884s ---- 884s 54 pairs aligned 0 times concordantly or discordantly; of these: 884s 108 mates make up the pairs; of these: 884s 94 (87.04%) aligned 0 times 884s 9 (8.33%) aligned exactly 1 time 884s 5 (4.63%) aligned >1 times 884s 14.55% overall alignment rate 884s Read 50 alignments... 884s Read 100 alignments... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s ACAA 884s ACAA 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s GA 884s GA 884s Processing line... 884s /usr/bin/bowtie2 --n-ceil 0.91504050943928,1.27976118553416 --ma 20.9393668388232 --score-min L,8.40087606249119,5.14307786857785 -k 4 --rfg 48.0996965926486,6.61880515543671 -N 1 -L29 --mm --cp-ival 2 --cp-min 3 -f -p 4 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 884s GA 884s GA 884s Processing line... 884s GA 884s GA 884s Processing line... 884s GA 884s GA 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s AAAGAGGCGGGG 884s AAAGAGGCGGGG 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s GCGAT 884s GCGAT 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s ACTCTTTACACAAAGAGGCGGGGTAACATTCAGCT 884s ACTCTTTACACAAAGAGGCGGGGTAACATTCAGCT 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s ATGACTCTTTACA 884s ATGACTCTTTACA 884s Processing line... 884s Processing line... 884s TAACAT 884s TAACAT 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s CAAAGAGGCGGGGTAACATTCAGCT 884s CAAAGAGGCGGGGTAACATTCAGCT 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s CATG 884s CATG 884s Processing line... 884s CATG 884s CATG 884s Processing line... 884s Processing line... 884s AC 884s AC 884s Processing line... 884s AC 884s AC 884s Processing line... 884s AC 884s AC 884s Processing line... 884s AC 884s AC 884s Processing line... 884s Processing line... 884s GGG 884s GGG 884s Processing line... 884s GGG 884s GGG 884s Processing line... 884s GGG 884s GGG 884s Processing line... 884s GGG 884s GGG 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s GTGT 884s GTGT 884s Processing line... 884s ACAC 884s ACAC 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s AGAGGCGGGGTAAC 884s AGAGGCGGGGTAAC 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s GTACAT 884s GTACAT 884s Processing line... 884s Processing line... 884s Processing line... 884s Processing line... 884s ACATGACTCTT 884s ACATGACTCTT 884s Processing line... 884s GAGGCGG 884s GAGGCGG 884s --- Summary --- 884s Read 1 reference strings 884s Checked 27 alignments, 0 edits 884s --------------- 884s PASSED 884s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 884s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 884s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (1) 884s Warning: skipping mate #1 of read '37' because it was < 2 characters long 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 884s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 884s 55 reads; of these: 884s 55 (100.00%) were paired; of these: 884s 54 (98.18%) aligned concordantly 0 times 884s 1 (1.82%) aligned concordantly exactly 1 time 884s 0 (0.00%) aligned concordantly >1 times 884s ---- 884s 54 pairs aligned concordantly 0 times; of these: 884s 0 (0.00%) aligned discordantly 1 time 884s ---- 884s 54 pairs aligned 0 times concordantly or discordantly; of these: 884s 108 mates make up the pairs; of these: 884s 94 (87.04%) aligned 0 times 884s 9 (8.33%) aligned exactly 1 time 884s 5 (4.63%) aligned >1 times 884s 14.55% overall alignment rate 884s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 884s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 884s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 884s Flattened IUPAC characters 884s Mutating sequence Sim.pm.1 884s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 884s Finished SNPs 884s Finished ref gaps 884s Finished read gaps 884s Mutating sequence Sim.pm.2 884s Introducing 1 SNPs, 2/0 ref/read gaps, and 1 rearrangements 884s Finished SNPs 884s Finished ref gaps 884s Finished read gaps 884s Mutated reference genome to subject genome 884s SNPs introduced: 1 884s Reference gaps introduced: 3 884s Read gaps introduced: 0 884s Rearrangements introduced: 2 884s Created read sampler 884s Sampling 67 reads 884s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 884s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 884s parsing sequence Sim.pm.1... 884s parsing sequence Sim.pm.2... 884s *** Run 12 of 100 884s /usr/bin/bowtie2 -k 6 --score-min L,2.79326297968037,6.76198528603127 --local --cp-ival 2 --cp-min 2 -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 884s Parsed 74 reference bases 885s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 885s Warning: skipping read '8' because it was < 2 characters long 885s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 885s Warning: skipping read '12' because it was < 2 characters long 885s 67 reads; of these: 885s 67 (100.00%) were unpaired; of these: 885s 67 (100.00%) aligned 0 times 885s 0 (0.00%) aligned exactly 1 time 885s 0 (0.00%) aligned >1 times 885s 0.00% overall alignment rate 885s Read 50 alignments... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s --- Summary --- 885s Read 1 reference strings 885s Checked 0 alignments, 0 edits 885s --------------- 885s PASSED 885s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 885s /usr/bin/bowtie2 -k 6 --score-min L,2.79326297968037,6.76198528603127 --local --cp-ival 2 --cp-min 2 -r -p 2 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 885s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 885s Warning: skipping read '8' because it was < 2 characters long 885s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 885s Warning: skipping read '12' because it was < 2 characters long 885s 67 reads; of these: 885s 67 (100.00%) were unpaired; of these: 885s 67 (100.00%) aligned 0 times 885s 0 (0.00%) aligned exactly 1 time 885s 0 (0.00%) aligned >1 times 885s 0.00% overall alignment rate 885s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 885s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 885s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 885s *** Run 13 of 100 885s /usr/bin/bowtie2 --score-min L,8.56918085011671,5.12417693182595 -k 3 --ma 9.58432326962588 --rfg 2.88252073201084 --trim3 0 --mm --cp-ival 2 --nofw --cp-min 3 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 885s Flattened IUPAC characters 885s Mutating sequence Sim.pm.2 885s Introducing 13 SNPs, 1/0 ref/read gaps, and 0 rearrangements 885s Finished SNPs 885s Finished ref gaps 885s Finished read gaps 885s Mutating sequence Sim.pm.1 885s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 885s Finished SNPs 885s Finished ref gaps 885s Finished read gaps 885s Mutated reference genome to subject genome 885s SNPs introduced: 15 885s Reference gaps introduced: 2 885s Read gaps introduced: 0 885s Rearrangements introduced: 0 885s Created read sampler 885s Sampling 35 reads 885s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 885s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 885s parsing sequence Sim.pm.1... 885s parsing sequence Sim.pm.2... 885s Parsed 74 reference bases 885s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 885s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 885s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 885s Warning: skipping read '11' because it was < 2 characters long 885s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 885s 35 reads; of these: 885s 35 (100.00%) were unpaired; of these: 885s 31 (88.57%) aligned 0 times 885s 2 (5.71%) aligned exactly 1 time 885s 2 (5.71%) aligned >1 times 885s 11.43% overall alignment rate 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s CC 885s CC 885s Processing line... 885s CC 885s CC 885s Processing line... 885s Processing line... 885s Processing line... 885s ACA 885s ACA 885s Processing line... 885s ACA 885s ACA 885s Processing line... 885s ACA 885s ACA 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s GAGGCGGGGTAACATTC 885s GAGGCGGGGTAACATTC 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s Processing line... 885s CATTC 885s CATTC 885s Processing line... 885s Processing line... 885s --- Summary --- 885s Read 1 reference strings 885s Checked 7 alignments, 0 edits 885s --------------- 885s PASSED 885s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 885s /usr/bin/bowtie2 --score-min L,8.56918085011671,5.12417693182595 -k 3 --ma 9.58432326962588 --rfg 2.88252073201084 --trim3 0 --mm --cp-ival 2 --nofw --cp-min 3 -q -p 4 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 885s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 885s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 885s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 885s Warning: skipping read '11' because it was < 2 characters long 885s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 885s 35 reads; of these: 885s 35 (100.00%) were unpaired; of these: 885s 31 (88.57%) aligned 0 times 885s 2 (5.71%) aligned exactly 1 time 885s 2 (5.71%) aligned >1 times 885s 11.43% overall alignment rate 885s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 885s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 885s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 885s /usr/bin/bowtie2 --score-min L,8.56918085011671,5.12417693182595 -k 3 --ma 9.58432326962588 --rfg 2.88252073201084 --trim3 0 --mm --cp-ival 2 --nofw --cp-min 3 -q -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 885s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 885s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 885s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 885s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 885s Warning: skipping read '11' because it was < 2 characters long 885s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 885s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 885s 35 reads; of these: 885s 35 (100.00%) were unpaired; of these: 885s 31 (88.57%) aligned 0 times 885s 2 (5.71%) aligned exactly 1 time 885s 2 (5.71%) aligned >1 times 885s 11.43% overall alignment rate 885s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 885s Flattened IUPAC characters 885s Mutating sequence Sim.pm.1 885s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 885s Finished SNPs 885s Finished ref gaps 885s Finished read gaps 885s Mutating sequence Sim.pm.2 885s Introducing 12 SNPs, 0/1 ref/read gaps, and 0 rearrangements 885s Finished SNPs 885s Finished ref gaps 885s Finished read gaps 885s Mutated reference genome to subject genome 885s SNPs introduced: 13 885s Reference gaps introduced: 0 885s Read gaps introduced: 1 885s Rearrangements introduced: 1 885s Created read sampler 885s Sampling 107 reads 885s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 885s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 885s parsing sequence Sim.pm.1... 885s parsing sequence Sim.pm.2... 885s Parsed 74 reference bases 885s *** Run 14 of 100 885s /usr/bin/bowtie2 --ma 28.43649219866 -a --mp 8.21745208114545,3.03501714299268 --rdg 12.412553294593,2.25198063925763 --cp-ival 1 --cp-min 5 --n-ceil 1.36842628583137,0.963715205162667 --score-min L,3.33748839455029,5.29297089572182 -R 2 --nofw --norc -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 886s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 886s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #1 of read '8' because it was < 2 characters long 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 886s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #1 of read '27' because it was < 2 characters long 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 886s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #1 of read '38' because it was < 2 characters long 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 886s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #2 of read '47' because it was < 2 characters long 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 886s Warning: skipping mate #1 of read '58' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #1 of read '58' because it was < 2 characters long 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 886s Read 50 alignments... 886s Read 100 alignments... 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 886s 107 reads; of these: 886s 107 (100.00%) were paired; of these: 886s 107 (100.00%) aligned concordantly 0 times 886s 0 (0.00%) aligned concordantly exactly 1 time 886s 0 (0.00%) aligned concordantly >1 times 886s ---- 886s 107 pairs aligned concordantly 0 times; of these: 886s 0 (0.00%) aligned discordantly 1 time 886s ---- 886s 107 pairs aligned 0 times concordantly or discordantly; of these: 886s 214 mates make up the pairs; of these: 886s 214 (100.00%) aligned 0 times 886s 0 (0.00%) aligned exactly 1 time 886s 0 (0.00%) aligned >1 times 886s 0.00% overall alignment rate 886s Read 150 alignments... 886s Read 200 alignments... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s /usr/bin/bowtie2 --ma 28.43649219866 -a --mp 8.21745208114545,3.03501714299268 --rdg 12.412553294593,2.25198063925763 --cp-ival 1 --cp-min 5 --n-ceil 1.36842628583137,0.963715205162667 --score-min L,3.33748839455029,5.29297089572182 -R 2 --nofw --norc -q -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s --- Summary --- 886s Read 1 reference strings 886s Checked 0 alignments, 0 edits 886s --------------- 886s PASSED 886s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 886s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 886s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #1 of read '8' because it was < 2 characters long 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 886s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #1 of read '27' because it was < 2 characters long 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 886s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #1 of read '38' because it was < 2 characters long 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 886s Warning: skipping mate #1 of read '58' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #1 of read '58' because it was < 2 characters long 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 886s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #2 of read '47' because it was < 2 characters long 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 886s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 886s 107 reads; of these: 886s 107 (100.00%) were paired; of these: 886s 107 (100.00%) aligned concordantly 0 times 886s 0 (0.00%) aligned concordantly exactly 1 time 886s 0 (0.00%) aligned concordantly >1 times 886s ---- 886s 107 pairs aligned concordantly 0 times; of these: 886s 0 (0.00%) aligned discordantly 1 time 886s ---- 886s 107 pairs aligned 0 times concordantly or discordantly; of these: 886s 214 mates make up the pairs; of these: 886s 214 (100.00%) aligned 0 times 886s 0 (0.00%) aligned exactly 1 time 886s 0 (0.00%) aligned >1 times 886s 0.00% overall alignment rate 886s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 886s Flattened IUPAC characters 886s Mutating sequence Sim.pm.2 886s Introducing 7 SNPs, 3/1 ref/read gaps, and 2 rearrangements 886s Finished SNPs 886s Finished ref gaps 886s Finished read gaps 886s Mutating sequence Sim.pm.1 886s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 886s Finished SNPs 886s Finished ref gaps 886s Finished read gaps 886s Mutated reference genome to subject genome 886s SNPs introduced: 8 886s Reference gaps introduced: 3 886s Read gaps introduced: 1 886s Rearrangements introduced: 2 886s Created read sampler 886s Sampling 108 reads 886s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 886s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 886s parsing sequence Sim.pm.1... 886s *** Run 15 of 100 886s /usr/bin/bowtie2 --score-min L,9.82160487158057,3.00300366536496 --local --cp-ival 1 --mm --cp-min 3 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 886s parsing sequence Sim.pm.2... 886s Parsed 74 reference bases 886s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #1 of read '12' because it was < 2 characters long 886s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #2 of read '58' because it was < 2 characters long 886s Read 50 alignments... 886s Read 100 alignments... 886s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #2 of read '77' because it was < 2 characters long 886s Warning: skipping mate #1 of read '93' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #1 of read '93' because it was < 2 characters long 886s Warning: skipping mate #2 of read '93' because it was < 2 characters long 886s Warning: skipping mate #2 of read '100' because length (1) <= # seed mismatches (0) 886s Warning: skipping mate #2 of read '100' because it was < 2 characters long 886s 108 reads; of these: 886s 108 (100.00%) were paired; of these: 886s 108 (100.00%) aligned concordantly 0 times 886s 0 (0.00%) aligned concordantly exactly 1 time 886s 0 (0.00%) aligned concordantly >1 times 886s ---- 886s 108 pairs aligned concordantly 0 times; of these: 886s 0 (0.00%) aligned discordantly 1 time 886s ---- 886s 108 pairs aligned 0 times concordantly or discordantly; of these: 886s 216 mates make up the pairs; of these: 886s 216 (100.00%) aligned 0 times 886s 0 (0.00%) aligned exactly 1 time 886s 0 (0.00%) aligned >1 times 886s 0.00% overall alignment rate 886s Read 150 alignments... 886s Read 200 alignments... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s Processing line... 886s --- Summary --- 886s Read 1 reference strings 886s Checked 0 alignments, 0 edits 886s --------------- 886s PASSED 886s Flattened IUPAC characters 886s Mutating sequence Sim.pm.2 886s Introducing 14 SNPs, 0/1 ref/read gaps, and 0 rearrangements 886s Finished SNPs 886s Finished ref gaps 886s Finished read gaps 886s Mutating sequence Sim.pm.1 886s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 886s Finished SNPs 886s Finished ref gaps 886s Finished read gaps 886s Mutated reference genome to subject genome 886s SNPs introduced: 19 886s Reference gaps introduced: 0 886s Read gaps introduced: 1 886s Rearrangements introduced: 0 886s Created read sampler 886s Sampling 46 reads 886s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 886s *** Run 16 of 100 886s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mp 9.22338477661261,7.69024494368156 --trim3 1 -a --np 9 --nofw --rfg 22.2279038263354,3.06384520112855 --score-min L,6.98987416324173,9.70068891465597 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq 886s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 886s parsing sequence Sim.pm.1... 886s parsing sequence Sim.pm.2... 886s Parsed 74 reference bases 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 887s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 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 887s 46 reads; of these: 887s 46 (100.00%) were unpaired; of these: 887s 40 (86.96%) aligned 0 times 887s 6 (13.04%) aligned exactly 1 time 887s 0 (0.00%) aligned >1 times 887s 13.04% overall alignment rate 887s Read 50 alignments... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s ATG 887s ATG 887s Processing line... 887s Processing line... 887s CATA 887s CATA 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s AGGGCGATAAG 887s AGGGCGATAAG 887s Processing line... 887s Processing line... 887s Processing line... 887s GGGG 887s GGGG 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s GCGG 887s GCGG 887s Processing line... 887s Processing line... 887s Processing line... 887s ATG 887s ATG 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s --- Summary --- 887s Read 1 reference strings 887s Checked 6 alignments, 0 edits 887s --------------- 887s PASSED 887s *** Run 17 of 100 887s /usr/bin/bowtie2 --n-ceil 0.460006883647565,0.691744942589812 --score-min L,6.51849051568271,8.03098453424577 --trim5 5 --mm --cp-ival 1 --cp-min 2 -M 2 --rdg 15.5656762952369,6.30244619571973 --local -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 887s Flattened IUPAC characters 887s Mutating sequence Sim.pm.1 887s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 887s Finished SNPs 887s Finished ref gaps 887s Finished read gaps 887s Mutating sequence Sim.pm.2 887s Introducing 12 SNPs, 1/0 ref/read gaps, and 0 rearrangements 887s Finished SNPs 887s Finished ref gaps 887s Finished read gaps 887s Mutated reference genome to subject genome 887s SNPs introduced: 12 887s Reference gaps introduced: 1 887s Read gaps introduced: 0 887s Rearrangements introduced: 1 887s Created read sampler 887s Sampling 28 reads 887s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 887s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 887s parsing sequence Sim.pm.1... 887s parsing sequence Sim.pm.2... 887s Parsed 74 reference bases 887s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 887s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 887s Warning: skipping read '7' because it was < 2 characters long 887s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 887s Warning: skipping read '13' because it was < 2 characters long 887s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 887s Warning: skipping read '19' because it was < 2 characters long 887s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 887s Warning: skipping read '24' because it was < 2 characters long 887s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 887s Warning: skipping read '26' because it was < 2 characters long 887s 28 reads; of these: 887s 28 (100.00%) were unpaired; of these: 887s 28 (100.00%) aligned 0 times 887s 0 (0.00%) aligned exactly 1 time 887s 0 (0.00%) aligned >1 times 887s 0.00% overall alignment rate 887s /usr/bin/bowtie2 --n-ceil 0.460006883647565,0.691744942589812 --score-min L,6.51849051568271,8.03098453424577 --trim5 5 --mm --cp-ival 1 --cp-min 2 -M 2 --rdg 15.5656762952369,6.30244619571973 --local -f -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s --- Summary --- 887s Read 1 reference strings 887s Checked 0 alignments, 0 edits 887s --------------- 887s PASSED 887s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 887s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 887s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 887s Warning: skipping read '7' because it was < 2 characters long 887s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 887s Warning: skipping read '13' because it was < 2 characters long 887s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 887s Warning: skipping read '19' because it was < 2 characters long 887s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 887s Warning: skipping read '24' because it was < 2 characters long 887s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 887s Warning: skipping read '26' because it was < 2 characters long 887s 28 reads; of these: 887s 28 (100.00%) were unpaired; of these: 887s 28 (100.00%) aligned 0 times 887s 0 (0.00%) aligned exactly 1 time 887s 0 (0.00%) aligned >1 times 887s 0.00% overall alignment rate 887s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 887s Flattened IUPAC characters 887s Mutating sequence Sim.pm.2 887s Introducing 2 SNPs, 0/1 ref/read gaps, and 2 rearrangements 887s Finished SNPs 887s Finished ref gaps 887s Finished read gaps 887s Mutating sequence Sim.pm.1 887s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 887s Finished SNPs 887s Finished ref gaps 887s Finished read gaps 887s *** Run 18 of 100 887s /usr/bin/bowtie2 -R 4 --np 10 --score-min L,6.94185840387734,6.3217594955813 --rfg 3.01307180948141,6.48629279729672 --cp-ival 1 --cp-min 2 -k 7 --ma 31.9555264535452 --trim3 2 --mp 9.79687494539394,4.89249597250585 -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw 887s Mutated reference genome to subject genome 887s SNPs introduced: 10 887s Reference gaps introduced: 0 887s Read gaps introduced: 1 887s Rearrangements introduced: 2 887s Created read sampler 887s Sampling 90 reads 887s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 887s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 887s parsing sequence Sim.pm.1... 887s parsing sequence Sim.pm.2... 887s Parsed 74 reference bases 887s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 887s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 887s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 887s Warning: skipping mate #1 of read '3' because it was < 2 characters long 887s Warning: skipping mate #2 of read '3' because it was < 2 characters long 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 887s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 887s Warning: skipping mate #1 of read '5' because it was < 2 characters long 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 887s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 887s Warning: skipping mate #2 of read '17' because it was < 2 characters long 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 887s Read 50 alignments... 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 887s Read 100 alignments... 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 887s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 887s Warning: skipping mate #1 of read '55' because it was < 2 characters long 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 887s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 887s Warning: skipping mate #2 of read '56' because it was < 2 characters long 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 887s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 887s Warning: skipping mate #2 of read '68' because it was < 2 characters long 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 887s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 887s Warning: skipping mate #1 of read '72' because it was < 2 characters long 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 887s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 887s Warning: skipping mate #1 of read '86' because it was < 2 characters long 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 887s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 887s Warning: skipping mate #2 of read '87' because it was < 2 characters long 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 887s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 887s 90 reads; of these: 887s 88 (97.78%) were paired; of these: 887s 87 (98.86%) aligned concordantly 0 times 887s 1 (1.14%) aligned concordantly exactly 1 time 887s 0 (0.00%) aligned concordantly >1 times 887s ---- 887s 87 pairs aligned concordantly 0 times; of these: 887s 0 (0.00%) aligned discordantly 1 time 887s ---- 887s 87 pairs aligned 0 times concordantly or discordantly; of these: 887s 174 mates make up the pairs; of these: 887s 145 (83.33%) aligned 0 times 887s 23 (13.22%) aligned exactly 1 time 887s 6 (3.45%) aligned >1 times 887s 2 (2.22%) were unpaired; of these: 887s 0 (0.00%) aligned 0 times 887s 2 (100.00%) aligned exactly 1 time 887s 0 (0.00%) aligned >1 times 887s 18.54% overall alignment rate 887s Read 150 alignments... 887s Read 200 alignments... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s ACA 887s ACA 887s Processing line... 887s ACA 887s ACA 887s Processing line... 887s TGT 887s TGT 887s Processing line... 887s ACA 887s ACA 887s Processing line... 887s ACA 887s ACA 887s Processing line... 887s ACA 887s ACA 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s CTCTTTACACAAAGAGGCGG 887s CTCTTTACACAAAGAGGCGG 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s GGCG 887s GGCG 887s Processing line... 887s GGCG 887s GGCG 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s Processing line... 887s ACTCTTTA 887s ACTCTTTA 887s Processing line... 887s Processing line... 887s TACATGACTCTTTACACAAAGAGGCGGG 887s TACATGACTCTTTACACAAAGAGGCGGG 887s Processing line... 887s Processing line... 887s TTTACACAAAGAGGCGGGGTAACAT 887s TTTACACAAAGAGGCGGGGTAACAT 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s ACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCTACCA 887s ACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCTACCA 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s GACTCTTTACACAAAGAGGCGGGG 887s GACTCTTTACACAAAGAGGCGGGG 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s CA 887s CA 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s GAC 887s GAC 887s Processing line... 887s Processing line... 887s AGAGGCGGGG 887s AGAGGCGGGG 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s TACATGACTCTTTACACAAAGAGGCGGGGT 887s TACATGACTCTTTACACAAAGAGGCGGGGT 887s Processing line... 887s Processing line... 887s Processing line... 887s GTACATGACTCTTTACACAAAGAGGCGGGGT 887s GTACATGACTCTTTACACAAAGAGGCGGGGT 887s Processing line... 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s GG 887s GG 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s GGGTAACATTCAGCTACC 887s GGGTAACATTCAGCTACC 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s CTTTACACAAAGAGGCGGGGTAACATT 887s CTTTACACAAAGAGGCGGGGTAACATT 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s CACA 887s CACA 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s AAGAGGCGGGGTAACATTC 887s AAGAGGCGGGGTAACATTC 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s ACTCTTTACACAAAGAGGCGGGG 887s ACTCTTTACACAAAGAGGCGGGG 887s Processing line... 887s Processing line... 887s TGACTCTTTACACAAAGAGGCGGGGTAAC 887s TGACTCTTTACACAAAGAGGCGGGGTAAC 887s Processing line... 887s Processing line... 887s CACAAA 887s CACAAA 887s Processing line... 887s TGAC 887s TGAC 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s TCTTTACACAAAGAGGCGG 887s TCTTTACACAAAGAGGCGG 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s TTCAG 887s TTCAG 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s GGGTGTACAT 887s GGGTGTACAT 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s AAAGAGGCGGGGTAACA 887s AAAGAGGCGGGGTAACA 887s Processing line... 887s Processing line... 887s CATGACTCTTTACACAAAGAGGCGGGGTAAC 887s CATGACTCTTTACACAAAGAGGCGGGGTAAC 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s CTCTTTAC 887s CTCTTTAC 887s Processing line... 887s Processing line... 887s TTCAGCT 887s TTCAGCT 887s Processing line... 887s Processing line... 887s ACACAAAGAGGCGGGGTAA 887s ACACAAAGAGGCGGGGTAA 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s Processing line... 887s GGTAACATTCAGCTACCA 887s GGTAACATTCAGCTACCA 887s Processing line... 887s --- Summary --- 887s Read 1 reference strings 887s Checked 63 alignments, 0 edits 887s --------------- 887s PASSED 887s Flattened IUPAC characters 887s Mutating sequence Sim.pm.1 887s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 887s Finished SNPs 887s Finished ref gaps 887s Finished read gaps 887s Mutating sequence Sim.pm.2 887s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 887s Finished SNPs 887s Finished ref gaps 887s Finished read gaps 887s Mutated reference genome to subject genome 887s SNPs introduced: 5 887s Reference gaps introduced: 0 887s Read gaps introduced: 0 887s Rearrangements introduced: 1 887s Created read sampler 887s Sampling 126 reads 887s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 887s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 887s parsing sequence Sim.pm.1... 887s parsing sequence Sim.pm.2... 887s Parsed 74 reference bases 887s *** Run 19 of 100 887s /usr/bin/bowtie2 --cp-min 3 --cp-ival 2 --mp 9.61650685938219,3.0670651917814 -M 6 --np 1 -R 3 --trim5 1 --rfg 41.6562663576485,19.22194069152 --gbar 1 --score-min L,5.96027071244224,3.02020841078726 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 888s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 888s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '16' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 888s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '20' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 888s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 888s Warning: skipping mate #2 of read '50' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 888s Read 50 alignments... 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 888s Read 100 alignments... 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 888s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '89' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 888s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '93' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 888s Read 150 alignments... 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 888s 126 reads; of these: 888s 124 (98.41%) were paired; of these: 888s 122 (98.39%) aligned concordantly 0 times 888s 0 (0.00%) aligned concordantly exactly 1 time 888s 2 (1.61%) aligned concordantly >1 times 888s ---- 888s 122 pairs aligned concordantly 0 times; of these: 888s 1 (0.82%) aligned discordantly 1 time 888s ---- 888s 121 pairs aligned 0 times concordantly or discordantly; of these: 888s 242 mates make up the pairs; of these: 888s 191 (78.93%) aligned 0 times 888s 37 (15.29%) aligned exactly 1 time 888s 14 (5.79%) aligned >1 times 888s 2 (1.59%) were unpaired; of these: 888s 2 (100.00%) aligned 0 times 888s 0 (0.00%) aligned exactly 1 time 888s 0 (0.00%) aligned >1 times 888s 22.80% overall alignment rate 888s Read 200 alignments... 888s Read 250 alignments... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GGGTGTACATGA 888s GGGTGTACATGA 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s TAAC 888s TAAC 888s Processing line... 888s Processing line... 888s Processing line... 888s ACACAAAGAGGCGGGGTAACATTCA 888s ACACAAAGAGGCGGGGTAACATTCA 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GACTCTTTAC 888s GACTCTTTAC 888s Processing line... 888s Processing line... 888s AT 888s AT 888s Processing line... 888s AGAGGCGGGGTAACATTCAGCTA 888s AGAGGCGGGGTAACATTCAGCTA 888s Processing line... 888s Processing line... 888s Processing line... 888s CACAA 888s CACAA 888s Processing line... 888s Processing line... 888s GTACATGACTCTTT 888s GTACATGACTCTTT 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s CAAAGAGGCGGGGTAACATT 888s CAAAGAGGCGGGGTAACATT 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s CTCTTTACAC 888s CTCTTTACAC 888s Processing line... 888s Processing line... 888s Processing line... 888s GGGTGTAC 888s GGGTGTAC 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s AAGAG 888s AAGAG 888s Processing line... 888s Processing line... 888s ACA 888s ACA 888s Processing line... 888s GCTA 888s GCTA 888s Processing line... 888s AGAGG 888s AGAGG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GAGGC 888s GAGGC 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s CACAAAGAG 888s CACAAAGAG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s TTTACACAAAGAGGCGGGGTAACATTC 888s TTTACACAAAGAGGCGGGGTAACATTC 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s CCA 888s CCA 888s Processing line... 888s Processing line... 888s TACATGACTCTTTACACAAAGAGGCGGG 888s TACATGACTCTTTACACAAAGAGGCGGG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GACTCTTTACACA 888s GACTCTTTACACA 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GGCG 888s GGCG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s AC 888s AC 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GGTGTAC 888s GGTGTAC 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GG 888s GG 888s Processing line... 888s Processing line... 888s ACTCTTTACACAA 888s ACTCTTTACACAA 888s Processing line... 888s Processing line... 888s TGTACATGACTCTTT 888s TGTACATGACTCTTT 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s CATTCA 888s CATTCA 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s CAAAGAGGCGGGG 888s CAAAGAGGCGGGG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s TGTAC 888s TGTAC 888s Processing line... 888s Processing line... 888s CAG 888s CAG 888s Processing line... 888s Processing line... 888s TGTACATGACTCTTTACACAAAGA 888s TGTACATGACTCTTTACACAAAGA 888s Processing line... 888s Processing line... 888s ACTCTTTACACAAAG 888s ACTCTTTACACAAAG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s CTTTACACAAAG 888s CTTTACACAAAG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GCC 888s GCC 888s Processing line... 888s Processing line... 888s GAT 888s GAT 888s Processing line... 888s Processing line... 888s CACAAAGAGGCG 888s CACAAAGAGGCG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s CG 888s CG 888s Processing line... 888s Processing line... 888s GCGGGG 888s GCGGGG 888s Processing line... 888s CGGGG 888s CGGGG 888s Processing line... 888s GTAACATTCA 888s GTAACATTCA 888s Processing line... 888s GAG 888s GAG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GG 888s GG 888s Processing line... 888s Processing line... 888s AGC 888s AGC 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s AAC 888s AAC 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GTACATGACTCTTTACACA 888s GTACATGACTCTTTACACA 888s Processing line... 888s AG 888s AG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GGGGTAACATTCAG 888s GGGGTAACATTCAG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s TACATG 888s TACATG 888s Processing line... 888s Processing line... 888s CGGGGTA 888s CGGGGTA 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s CACAAAGAG 888s CACAAAGAG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GGGTAA 888s GGGTAA 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s GAGG 888s GAGG 888s Processing line... 888s Processing line... 888s TAACA 888s TAACA 888s /usr/bin/bowtie2 --cp-min 3 --cp-ival 2 --mp 9.61650685938219,3.0670651917814 -M 6 --np 1 -R 3 --trim5 1 --rfg 41.6562663576485,19.22194069152 --gbar 1 --score-min L,5.96027071244224,3.02020841078726 -q -p 4 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s CACAAAGAGGCG 888s CACAAAGAGGCG 888s Processing line... 888s GG 888s GG 888s Processing line... 888s Processing line... 888s Processing line... 888s TCAG 888s TCAG 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s Processing line... 888s --- Summary --- 888s Read 1 reference strings 888s Checked 57 alignments, 0 edits 888s --------------- 888s PASSED 888s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 888s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 888s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '16' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 888s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '89' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 888s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 888s Warning: skipping mate #2 of read '50' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 888s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '20' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 888s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '93' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 888s 126 reads; of these: 888s 124 (98.41%) were paired; of these: 888s 122 (98.39%) aligned concordantly 0 times 888s 0 (0.00%) aligned concordantly exactly 1 time 888s 2 (1.61%) aligned concordantly >1 times 888s ---- 888s 122 pairs aligned concordantly 0 times; of these: 888s 1 (0.82%) aligned discordantly 1 time 888s ---- 888s 121 pairs aligned 0 times concordantly or discordantly; of these: 888s 242 mates make up the pairs; of these: 888s 191 (78.93%) aligned 0 times 888s 37 (15.29%) aligned exactly 1 time 888s 14 (5.79%) aligned >1 times 888s 2 (1.59%) were unpaired; of these: 888s 2 (100.00%) aligned 0 times 888s 0 (0.00%) aligned exactly 1 time 888s 0 (0.00%) aligned >1 times 888s 22.80% overall alignment rate 888s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 888s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 888s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 888s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 888s /usr/bin/bowtie2 --cp-min 3 --cp-ival 2 --mp 9.61650685938219,3.0670651917814 -M 6 --np 1 -R 3 --trim5 1 --rfg 41.6562663576485,19.22194069152 --gbar 1 --score-min L,5.96027071244224,3.02020841078726 -q -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 888s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 888s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '20' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 888s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '16' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 888s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 888s Warning: skipping mate #2 of read '50' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 888s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '89' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 888s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 888s Warning: skipping mate #1 of read '93' because it was < 2 characters long 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 888s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 888s 126 reads; of these: 888s 124 (98.41%) were paired; of these: 888s 122 (98.39%) aligned concordantly 0 times 888s 0 (0.00%) aligned concordantly exactly 1 time 888s 2 (1.61%) aligned concordantly >1 times 888s ---- 888s 122 pairs aligned concordantly 0 times; of these: 888s 1 (0.82%) aligned discordantly 1 time 888s ---- 888s 121 pairs aligned 0 times concordantly or discordantly; of these: 888s 242 mates make up the pairs; of these: 888s 191 (78.93%) aligned 0 times 888s 37 (15.29%) aligned exactly 1 time 888s 14 (5.79%) aligned >1 times 888s 2 (1.59%) were unpaired; of these: 888s 2 (100.00%) aligned 0 times 888s 0 (0.00%) aligned exactly 1 time 888s 0 (0.00%) aligned >1 times 888s 22.80% overall alignment rate 888s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 888s Flattened IUPAC characters 888s Mutating sequence Sim.pm.2 888s Introducing 12 SNPs, 1/2 ref/read gaps, and 0 rearrangements 888s Finished SNPs 888s Finished ref gaps 888s Finished read gaps 888s Mutating sequence Sim.pm.1 888s Introducing 8 SNPs, 0/0 ref/read gaps, and 2 rearrangements 888s Finished SNPs 888s Finished ref gaps 888s Finished read gaps 888s Mutated reference genome to subject genome 888s SNPs introduced: 20 888s Reference gaps introduced: 1 888s Read gaps introduced: 2 888s Rearrangements introduced: 2 888s Created read sampler 888s Sampling 150 reads 888s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 888s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 888s parsing sequence Sim.pm.1... 888s parsing sequence Sim.pm.2... 888s Parsed 74 reference bases 888s *** Run 20 of 100 888s /usr/bin/bowtie2 -k 6 --ma 25.8472165246557 --cp-min 2 --mm --cp-ival 1 -i L,0.11178695014766 --gbar 2 --score-min L,1.42964782403785,3.64467594623447 --n-ceil 0.861935396569087,0.204913632673053 --nofw -R 2 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq 889s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s Read 50 alignments... 889s 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 889s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_135_135_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s Read 100 alignments... 889s 150 reads; of these: 889s 150 (100.00%) were unpaired; of these: 889s 133 (88.67%) aligned 0 times 889s 14 (9.33%) aligned exactly 1 time 889s 3 (2.00%) aligned >1 times 889s 11.33% overall alignment rate 889s Read 150 alignments... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s TCT 889s TCT 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s TC 889s TC 889s Processing line... 889s TC 889s TC 889s Processing line... 889s Processing line... 889s Processing line... 889s TTC 889s TTC 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s GGCC 889s GGCC 889s Processing line... 889s Processing line... 889s Processing line... 889s CGAA 889s CGAA 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s ACACAAAGAGG 889s ACACAAAGAGG 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s TTA 889s TTA 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s GTACATGACTCT 889s GTACATGACTCT 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s GAA 889s GAA 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s AAGAGGCGGGG 889s AAGAGGCGGGG 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s ACCA 889s ACCA 889s Processing line... 889s AGGCG 889s AGGCG 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s GTAACATTC 889s GTAACATTC 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s AAAG 889s AAAG 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s AT 889s AT 889s Processing line... 889s AT 889s AT 889s Processing line... 889s AT 889s AT 889s Processing line... 889s AT 889s AT 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s ATT 889s ATT 889s Processing line... 889s Processing line... 889s Processing line... 889s AA 889s AA 889s Processing line... 889s AA 889s AA 889s Processing line... 889s AA 889s AA 889s /usr/bin/bowtie2 -k 6 --ma 25.8472165246557 --cp-min 2 --mm --cp-ival 1 -i L,0.11178695014766 --gbar 2 --score-min L,1.42964782403785,3.64467594623447 --n-ceil 0.861935396569087,0.204913632673053 --nofw -R 2 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 889s Processing line... 889s AA 889s AA 889s Processing line... 889s AA 889s AA 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s Processing line... 889s --- Summary --- 889s Read 1 reference strings 889s Checked 25 alignments, 0 edits 889s --------------- 889s PASSED 889s ALSO checking that bowtie2 and bowtie2-align match up 889s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_135_135_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 889s /usr/bin/bowtie2 -k 6 --ma 25.8472165246557 --cp-min 2 --mm --cp-ival 1 -i L,0.11178695014766 --gbar 2 --score-min L,1.42964782403785,3.64467594623447 --n-ceil 0.861935396569087,0.204913632673053 --nofw -R 2 --qseq -p 2 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 889s 150 reads; of these: 889s 150 (100.00%) were unpaired; of these: 889s 133 (88.67%) aligned 0 times 889s 14 (9.33%) aligned exactly 1 time 889s 3 (2.00%) aligned >1 times 889s 11.33% overall alignment rate 889s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 889s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s Warning: skipping read 'R_1_1_1_135_135_1/1' because length (1) <= # seed mismatches (0) 889s Warning: skipping read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s 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 889s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 889s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 889s 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 889s 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 889s 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 889s 150 reads; of these: 889s 150 (100.00%) were unpaired; of these: 889s 133 (88.67%) aligned 0 times 889s 14 (9.33%) aligned exactly 1 time 889s 3 (2.00%) aligned >1 times 889s 11.33% overall alignment rate 889s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 889s Flattened IUPAC characters 889s Mutating sequence Sim.pm.1 889s Introducing 2 SNPs, 3/0 ref/read gaps, and 0 rearrangements 889s Finished SNPs 889s Finished ref gaps 889s Finished read gaps 889s Mutating sequence Sim.pm.2 889s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 889s Finished SNPs 889s Finished ref gaps 889s Finished read gaps 889s Mutated reference genome to subject genome 889s SNPs introduced: 7 889s Reference gaps introduced: 3 889s Read gaps introduced: 0 889s Rearrangements introduced: 1 889s Created read sampler 889s Sampling 121 reads 889s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 889s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 889s parsing sequence Sim.pm.1... 889s parsing sequence Sim.pm.2... 889s Parsed 74 reference bases 889s *** Run 21 of 100 889s /usr/bin/bowtie2 --n-ceil 1.46593646663455,1.09133252048086 --score-min L,5.54488063618301,1.30231718378931 --trim3 5 --mp 9.66463251807437,3.64035626101786 -N 1 -L26 --cp-ival 1 --cp-min 6 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 890s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '5' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 890s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 890s Warning: skipping read '6' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 890s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '17' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 890s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '18' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 890s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '26' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 890s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 890s Warning: skipping read '27' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 890s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '30' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 890s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '36' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 890s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '39' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 890s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '42' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 890s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '43' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 890s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '44' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 890s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #2 of read '46' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 890s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #2 of read '56' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 890s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '58' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 890s Read 50 alignments... 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 890s Read 100 alignments... 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 890s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '94' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 890s Warning: skipping mate #2 of read '95' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #2 of read '95' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 890s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '104' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 890s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '105' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 890s Warning: skipping mate #1 of read '106' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '106' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 890s Read 150 alignments... 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 890s 121 reads; of these: 890s 112 (92.56%) were paired; of these: 890s 109 (97.32%) aligned concordantly 0 times 890s 0 (0.00%) aligned concordantly exactly 1 time 890s 3 (2.68%) aligned concordantly >1 times 890s ---- 890s 109 pairs aligned concordantly 0 times; of these: 890s 2 (1.83%) aligned discordantly 1 time 890s ---- 890s 107 pairs aligned 0 times concordantly or discordantly; of these: 890s 214 mates make up the pairs; of these: 890s 191 (89.25%) aligned 0 times 890s 14 (6.54%) aligned exactly 1 time 890s 9 (4.21%) aligned >1 times 890s 9 (7.44%) were unpaired; of these: 890s 8 (88.89%) aligned 0 times 890s 0 (0.00%) aligned exactly 1 time 890s 1 (11.11%) aligned >1 times 890s 14.59% overall alignment rate 890s Read 200 alignments... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s ACACAAAG 890s ACACAAAG 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s GGTAAC 890s GGTAAC 890s Processing line... 890s Processing line... 890s TCTTT 890s TCTTT 890s Processing line... 890s GGG 890s GGG 890s Processing line... 890s CACAAAG 890s CACAAAG 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s AT 890s AT 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s TCTTTACACAAAGAGGCGG 890s TCTTTACACAAAGAGGCGG 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s GCG 890s GCG 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s AAGAGGCGGGGTA 890s AAGAGGCGGGGTA 890s Processing line... 890s TCTTTACACAAAGAGGC 890s TCTTTACACAAAGAGGC 890s Processing line... 890s AC 890s AC 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s CAT 890s CAT 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s AAGAGGC 890s AAGAGGC 890s Processing line... 890s ACA 890s ACA 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s CGA 890s CGA 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s CTCTTTACACAAAGAGGCGGGGTAACAT 890s CTCTTTACACAAAGAGGCGGGGTAACAT 890s Processing line... 890s ATG 890s ATG 890s Processing line... 890s Processing line... 890s Processing line... 890s TGTACATGACTCTTTACACAAAGAGGCG 890s TGTACATGACTCTTTACACAAAGAGGCG 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s CAAAGAGGCGGGGTA 890s CAAAGAGGCGGGGTA 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s GT 890s GT 890s Processing line... 890s Processing line... 890s TTACACAAAGAGGCGGGGTAA 890s TTACACAAAGAGGCGGGGTAA 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s ACATGACTCTTTAC 890s ACATGACTCTTTAC 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s GA 890s GA 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s ACATGACTCTTTACACAAA 890s ACATGACTCTTTACACAAA 890s Processing line... 890s Processing line... 890s AGAGGCGGGGTAAC 890s AGAGGCGGGGTAAC 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s GAGGCGGGGTAACATTCAG 890s GAGGCGGGGTAACATTCAG 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s /usr/bin/bowtie2 --n-ceil 1.46593646663455,1.09133252048086 --score-min L,5.54488063618301,1.30231718378931 --trim3 5 --mp 9.66463251807437,3.64035626101786 -N 1 -L26 --cp-ival 1 --cp-min 6 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s GGGT 890s GGGT 890s Processing line... 890s Processing line... 890s TACACAAAGAGGCG 890s TACACAAAGAGGCG 890s Processing line... 890s Processing line... 890s GG 890s GG 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s GGTAACATTCAGCTAC 890s GGTAACATTCAGCTAC 890s Processing line... 890s Processing line... 890s CAAAGAGGCGGGGTAACA 890s CAAAGAGGCGGGGTAACA 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s CAC 890s CAC 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s Processing line... 890s AGAGGCGGGGTAACATT 890s AGAGGCGGGGTAACATT 890s Processing line... 890s TACACAAAGAGGCGGGGTAACATTC 890s TACACAAAGAGGCGGGGTAACATTC 890s --- Summary --- 890s Read 1 reference strings 890s Checked 34 alignments, 0 edits 890s --------------- 890s PASSED 890s ALSO checking that bowtie2 and bowtie2-align match up 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 890s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '5' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 890s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 890s Warning: skipping read '6' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 890s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '17' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 890s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '18' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 890s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '26' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 890s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 890s Warning: skipping read '27' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 890s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '30' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 890s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '36' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 890s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '39' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 890s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '42' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 890s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '43' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 890s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '44' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 890s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #2 of read '46' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 890s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #2 of read '56' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 890s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '58' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 890s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '94' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 890s Warning: skipping mate #2 of read '95' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #2 of read '95' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 890s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '104' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 890s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '105' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 890s Warning: skipping mate #1 of read '106' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '106' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 890s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 890s 121 reads; of these: 890s 112 (92.56%) were paired; of these: 890s 109 (97.32%) aligned concordantly 0 times 890s 0 (0.00%) aligned concordantly exactly 1 time 890s 3 (2.68%) aligned concordantly >1 times 890s ---- 890s 109 pairs aligned concordantly 0 times; of these: 890s 2 (1.83%) aligned discordantly 1 time 890s ---- 890s 107 pairs aligned 0 times concordantly or discordantly; of these: 890s 214 mates make up the pairs; of these: 890s 191 (89.25%) aligned 0 times 890s 14 (6.54%) aligned exactly 1 time 890s 9 (4.21%) aligned >1 times 890s 9 (7.44%) were unpaired; of these: 890s 8 (88.89%) aligned 0 times 890s 0 (0.00%) aligned exactly 1 time 890s 1 (11.11%) aligned >1 times 890s 14.59% overall alignment rate 890s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 890s /usr/bin/bowtie2 --n-ceil 1.46593646663455,1.09133252048086 --score-min L,5.54488063618301,1.30231718378931 --trim3 5 --mp 9.66463251807437,3.64035626101786 -N 1 -L26 --cp-ival 1 --cp-min 6 -f -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 890s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '17' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 890s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '18' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 890s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '5' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 890s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 890s Warning: skipping read '6' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 890s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '36' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 890s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '39' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 890s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '42' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 890s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '43' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 890s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '44' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 890s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #2 of read '46' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 890s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '26' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 890s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 890s Warning: skipping read '27' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 890s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '30' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 890s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #2 of read '56' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 890s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '104' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 890s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '105' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 890s Warning: skipping mate #1 of read '106' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '106' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 890s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '94' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 890s Warning: skipping mate #2 of read '95' because length (1) <= # seed mismatches (1) 890s Warning: skipping mate #2 of read '95' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 890s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (1) 890s Warning: skipping mate #1 of read '58' because it was < 2 characters long 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 890s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 890s 121 reads; of these: 890s 112 (92.56%) were paired; of these: 890s 109 (97.32%) aligned concordantly 0 times 890s 0 (0.00%) aligned concordantly exactly 1 time 890s 3 (2.68%) aligned concordantly >1 times 890s ---- 890s 109 pairs aligned concordantly 0 times; of these: 890s 2 (1.83%) aligned discordantly 1 time 890s ---- 890s 107 pairs aligned 0 times concordantly or discordantly; of these: 890s 214 mates make up the pairs; of these: 890s 191 (89.25%) aligned 0 times 890s 14 (6.54%) aligned exactly 1 time 890s 9 (4.21%) aligned >1 times 890s 9 (7.44%) were unpaired; of these: 890s 8 (88.89%) aligned 0 times 890s 0 (0.00%) aligned exactly 1 time 890s 1 (11.11%) aligned >1 times 890s 14.59% overall alignment rate 890s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 890s Flattened IUPAC characters 890s Mutating sequence Sim.pm.2 890s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 890s Finished SNPs 890s Finished ref gaps 890s Finished read gaps 890s Mutating sequence Sim.pm.1 890s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 890s Finished SNPs 890s Finished ref gaps 890s Finished read gaps 890s Mutated reference genome to subject genome 890s SNPs introduced: 3 890s Reference gaps introduced: 0 890s Read gaps introduced: 0 890s Rearrangements introduced: 1 890s Created read sampler 890s Sampling 76 reads 890s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 890s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 890s parsing sequence Sim.pm.1... 890s parsing sequence Sim.pm.2... 890s Parsed 74 reference bases 890s *** Run 22 of 100 890s /usr/bin/bowtie2 --score-min L,4.74733689777722,4.7521741445804 --trim3 5 --rdg 8.5316146147378 --rfg 35.5438485672824,19.3047749907271 -i C,3.36344012333658 --cp-ival 1 -D 35 --cp-min 10 -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 891s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 891s Warning: skipping mate #1 of read '13' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 891s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 891s Warning: skipping mate #1 of read '17' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 891s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 891s Warning: skipping mate #1 of read '40' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 891s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 891s Warning: skipping mate #2 of read '45' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 891s Read 50 alignments... 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 891s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 891s Warning: skipping mate #1 of read '65' because it was < 2 characters long 891s Read 100 alignments... 891s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 891s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 891s Warning: skipping read '66' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 891s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 891s Warning: skipping mate #2 of read '71' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 891s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 891s Warning: skipping read '74' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 891s 76 reads; of these: 891s 64 (84.21%) were paired; of these: 891s 64 (100.00%) aligned concordantly 0 times 891s 0 (0.00%) aligned concordantly exactly 1 time 891s 0 (0.00%) aligned concordantly >1 times 891s ---- 891s 64 pairs aligned concordantly 0 times; of these: 891s 0 (0.00%) aligned discordantly 1 time 891s ---- 891s 64 pairs aligned 0 times concordantly or discordantly; of these: 891s 128 mates make up the pairs; of these: 891s 100 (78.12%) aligned 0 times 891s 20 (15.62%) aligned exactly 1 time 891s 8 (6.25%) aligned >1 times 891s 12 (15.79%) were unpaired; of these: 891s 10 (83.33%) aligned 0 times 891s 2 (16.67%) aligned exactly 1 time 891s 0 (0.00%) aligned >1 times 891s 21.43% overall alignment rate 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s GTACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCTACC 891s GTACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCTACC 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s GTGTACATGACTCTTTACACAAAGAGGCGGGGTA 891s GTGTACATGACTCTTTACACAAAGAGGCGGGGTA 891s Processing line... 891s Processing line... 891s TTCAGC 891s TTCAGC 891s Processing line... 891s Processing line... 891s TTTACACAAAGA 891s TTTACACAAAGA 891s Processing line... 891s Processing line... 891s GCGGGGTAACATT 891s GCGGGGTAACATT 891s Processing line... 891s Processing line... 891s GGG 891s GGG 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s CTTTA 891s CTTTA 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s AC 891s AC 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s AGAG 891s AGAG 891s Processing line... 891s Processing line... 891s TGTA 891s TGTA 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s CACAA 891s CACAA 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s GG 891s GG 891s Processing line... 891s Processing line... 891s GACTC 891s GACTC 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s GAGGCGGGGTAACA 891s GAGGCGGGGTAACA 891s Processing line... 891s Processing line... 891s Processing line... 891s TCTTTACACAAAGAGGCGGGGTAACATTC 891s TCTTTACACAAAGAGGCGGGGTAACATTC 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s ACATGAC 891s ACATGAC 891s Processing line... 891s Processing line... 891s Processing line... 891s TACACAA 891s TACACAA 891s Processing line... 891s /usr/bin/bowtie2 --score-min L,4.74733689777722,4.7521741445804 --trim3 5 --rdg 8.5316146147378 --rfg 35.5438485672824,19.3047749907271 -i C,3.36344012333658 --cp-ival 1 -D 35 --cp-min 10 -r -p 4 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 891s Processing line... 891s GTGTACATGACTCTTTACACAAAGAGGCGGGGTAACA 891s GTGTACATGACTCTTTACACAAAGAGGCGGGGTAACA 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s ATGACTCTTTACACAAAGAGGCGGGGTAA 891s ATGACTCTTTACACAAAGAGGCGGGGTAA 891s Processing line... 891s Processing line... 891s GGTGTACATGACTCTTTACACAAAGA 891s GGTGTACATGACTCTTTACACAAAGA 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s CACAAAGAGGC 891s CACAAAGAGGC 891s Processing line... 891s Processing line... 891s GGG 891s GGG 891s Processing line... 891s Processing line... 891s CGGGGTAACATT 891s CGGGGTAACATT 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s TCTTTACACAAAGAGGCGGGGTAACATTCAGCT 891s TCTTTACACAAAGAGGCGGGGTAACATTCAGCT 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s GTGTACATGA 891s GTGTACATGA 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s CTTTACACAAAGAGGC 891s CTTTACACAAAGAGGC 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s CA 891s CA 891s Processing line... 891s Processing line... 891s ACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCTAC 891s ACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCTAC 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s ACAAAGAGGC 891s ACAAAGAGGC 891s Processing line... 891s CCG 891s CCG 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s Processing line... 891s --- Summary --- 891s Read 1 reference strings 891s Checked 30 alignments, 0 edits 891s --------------- 891s PASSED 891s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 891s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 891s Warning: skipping mate #1 of read '17' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 891s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 891s Warning: skipping mate #1 of read '13' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 891s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 891s Warning: skipping mate #1 of read '65' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 891s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 891s Warning: skipping read '66' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 891s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 891s Warning: skipping mate #2 of read '71' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 891s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 891s Warning: skipping read '74' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 891s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 891s Warning: skipping mate #1 of read '40' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 891s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 891s Warning: skipping mate #2 of read '45' because it was < 2 characters long 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 891s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 891s 76 reads; of these: 891s 64 (84.21%) were paired; of these: 891s 64 (100.00%) aligned concordantly 0 times 891s 0 (0.00%) aligned concordantly exactly 1 time 891s 0 (0.00%) aligned concordantly >1 times 891s ---- 891s 64 pairs aligned concordantly 0 times; of these: 891s 0 (0.00%) aligned discordantly 1 time 891s ---- 891s 64 pairs aligned 0 times concordantly or discordantly; of these: 891s 128 mates make up the pairs; of these: 891s 100 (78.12%) aligned 0 times 891s 20 (15.62%) aligned exactly 1 time 891s 8 (6.25%) aligned >1 times 891s 12 (15.79%) were unpaired; of these: 891s 10 (83.33%) aligned 0 times 891s 2 (16.67%) aligned exactly 1 time 891s 0 (0.00%) aligned >1 times 891s 21.43% overall alignment rate 891s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 891s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 891s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 891s Flattened IUPAC characters 891s Mutating sequence Sim.pm.2 891s Introducing 15 SNPs, 3/0 ref/read gaps, and 0 rearrangements 891s Finished SNPs 891s Finished ref gaps 891s Finished read gaps 891s Mutating sequence Sim.pm.1 891s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 891s Finished SNPs 891s Finished ref gaps 891s Finished read gaps 891s Mutated reference genome to subject genome 891s SNPs introduced: 17 891s Reference gaps introduced: 4 891s Read gaps introduced: 0 891s Rearrangements introduced: 0 891s Created read sampler 891s Sampling 96 reads 891s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 891s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 891s parsing sequence Sim.pm.1... 891s parsing sequence Sim.pm.2... 891s Parsed 74 reference bases 891s *** Run 23 of 100 891s /usr/bin/bowtie2 --norc --np 1 --nofw --score-min L,8.03135845934296,4.61580789617434 --n-ceil 1.15186752793786,0.977363207878486 --cp-min 2 --cp-ival 1 --local --rdg 45.6774373797617,18.7336173035938 --mp 8.56807450171855,4.51865111109118 --trim3 9 -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw 891s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '1' because it was < 2 characters long 892s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '5' because it was < 2 characters long 892s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '14' because it was < 2 characters long 892s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '15' because it was < 2 characters long 892s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '19' because it was < 2 characters long 892s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '20' because it was < 2 characters long 892s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '24' because it was < 2 characters long 892s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '26' because it was < 2 characters long 892s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '39' because it was < 2 characters long 892s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '44' because it was < 2 characters long 892s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '54' because it was < 2 characters long 892s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '62' because it was < 2 characters long 892s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '64' because it was < 2 characters long 892s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '75' because it was < 2 characters long 892s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '78' because it was < 2 characters long 892s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '86' because it was < 2 characters long 892s Read 50 alignments... 892s Read 100 alignments... 892s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '89' because it was < 2 characters long 892s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 892s Warning: skipping mate #1 of read '93' because it was < 2 characters long 892s 96 reads; of these: 892s 78 (81.25%) were paired; of these: 892s 78 (100.00%) aligned concordantly 0 times 892s 0 (0.00%) aligned concordantly exactly 1 time 892s 0 (0.00%) aligned concordantly >1 times 892s ---- 892s 78 pairs aligned concordantly 0 times; of these: 892s 0 (0.00%) aligned discordantly 1 time 892s ---- 892s 78 pairs aligned 0 times concordantly or discordantly; of these: 892s 156 mates make up the pairs; of these: 892s 156 (100.00%) aligned 0 times 892s 0 (0.00%) aligned exactly 1 time 892s 0 (0.00%) aligned >1 times 892s 18 (18.75%) were unpaired; of these: 892s 18 (100.00%) aligned 0 times 892s 0 (0.00%) aligned exactly 1 time 892s 0 (0.00%) aligned >1 times 892s 0.00% overall alignment rate 892s Read 150 alignments... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s --- Summary --- 892s Read 1 reference strings 892s Checked 0 alignments, 0 edits 892s --------------- 892s PASSED 892s Flattened IUPAC characters 892s Mutating sequence Sim.pm.2 892s Introducing 7 SNPs, 2/2 ref/read gaps, and 0 rearrangements 892s Finished SNPs 892s Finished ref gaps 892s Finished read gaps 892s Mutating sequence Sim.pm.1 892s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 892s Finished SNPs 892s Finished ref gaps 892s Finished read gaps 892s Mutated reference genome to subject genome 892s SNPs introduced: 10 892s Reference gaps introduced: 2 892s Read gaps introduced: 3 892s Rearrangements introduced: 0 892s Created read sampler 892s Sampling 60 reads 892s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 892s *** Run 24 of 100 892s /usr/bin/bowtie2 --mp 8.15406213379245,7.35344565242663 --trim3 9 --cp-ival 3 --mm --cp-min 3 --score-min L,6.36658985082067,9.72057226917178 --n-ceil 1.31591708648622,0.391221951345851 --trim5 4 -R 3 -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 892s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 892s parsing sequence Sim.pm.1... 892s parsing sequence Sim.pm.2... 892s Parsed 74 reference bases 892s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 892s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '2' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 892s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '3' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 892s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '8' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 892s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 892s Warning: skipping read '9' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 892s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '10' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 892s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '12' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 892s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '13' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 892s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '15' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 892s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '16' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 892s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '18' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 892s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '30' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 892s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '31' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 892s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '35' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 892s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '36' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 892s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '38' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 892s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '44' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 892s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '45' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 892s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '47' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 892s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '53' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 892s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '54' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 892s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '58' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 892s 60 reads; of these: 892s 60 (100.00%) were unpaired; of these: 892s 54 (90.00%) aligned 0 times 892s 5 (8.33%) aligned exactly 1 time 892s 1 (1.67%) aligned >1 times 892s 10.00% overall alignment rate 892s Read 50 alignments... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s GGGTAACA 892s GGGTAACA 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s ACAAAG 892s ACAAAG 892s Processing line... 892s TACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCT 892s TACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCT 892s Processing line... 892s AA 892s AA 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s CGGGGTAACATTCAGCTACC 892s CGGGGTAACATTCAGCTACC 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s ACATGACTCTT 892s ACATGACTCTT 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s --- Summary --- 892s Read 1 reference strings 892s Checked 6 alignments, 0 edits 892s --------------- 892s PASSED 892s Flattened IUPAC characters 892s Mutating sequence Sim.pm.2 892s Introducing 9 SNPs, 0/1 ref/read gaps, and 1 rearrangements 892s Finished SNPs 892s Finished ref gaps 892s Finished read gaps 892s Mutating sequence Sim.pm.1 892s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 892s Finished SNPs 892s Finished ref gaps 892s Finished read gaps 892s Mutated reference genome to subject genome 892s SNPs introduced: 10 892s Reference gaps introduced: 0 892s Read gaps introduced: 1 892s Rearrangements introduced: 2 892s Created read sampler 892s Sampling 114 reads 892s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 892s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 892s parsing sequence Sim.pm.1... 892s parsing sequence Sim.pm.2... 892s Parsed 74 reference bases 892s *** Run 25 of 100 892s /usr/bin/bowtie2 --ma 16.5983141483072 --score-min L,4.2534914545467,1.04027453922822 --rdg 27.8064912918731 --trim3 8 --rfg 24.5493053447879,16.1027766017877 --mm --cp-ival 1 --cp-min 9 --np 2 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 892s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 892s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 892s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '2' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 892s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '7' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 892s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '8' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 892s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '11' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 892s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '18' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 892s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '21' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 892s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '22' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 892s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '24' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 892s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '28' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 892s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 892s Warning: skipping read '37' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 892s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '39' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 892s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '40' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 892s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '53' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 892s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '54' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 892s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '58' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 892s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '60' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 892s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '61' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 892s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '67' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 892s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '71' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 892s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '76' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 892s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '81' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 892s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '82' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 892s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '83' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 892s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '92' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 892s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '94' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 892s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '103' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 892s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '108' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 892s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '111' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 892s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '114' because it was < 2 characters long 892s 114 reads; of these: 892s 114 (100.00%) were unpaired; of these: 892s 103 (90.35%) aligned 0 times 892s 8 (7.02%) aligned exactly 1 time 892s 3 (2.63%) aligned >1 times 892s 9.65% overall alignment rate 892s Read 50 alignments... 892s Read 100 alignments... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s TAAGGGCCG 892s TAAGGGCCG 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s AT 892s AT 892s Processing line... 892s Processing line... 892s TTTACAC 892s TTTACAC 892s Processing line... 892s Processing line... 892s Processing line... 892s TACACAAAGAGGCG 892s TACACAAAGAGGCG 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s GGAGGGCGATAA 892s GGAGGGCGATAA 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s ATAAGGGCCGAACA 892s ATAAGGGCCGAACA 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s GG 892s GG 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s CATT 892s CATT 892s Processing line... 892s Processing line... 892s GAAC 892s GAAC 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s GGGTGTACATGACTCTT 892s GGGTGTACATGACTCTT 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s Processing line... 892s TG 892s TG 892s Processing line... 892s --- Summary --- 892s Read 1 reference strings 892s Checked 11 alignments, 0 edits 892s --------------- 892s PASSED 892s ALSO checking that bowtie2 and bowtie2-align match up 892s /usr/bin/bowtie2 --ma 16.5983141483072 --score-min L,4.2534914545467,1.04027453922822 --rdg 27.8064912918731 --trim3 8 --rfg 24.5493053447879,16.1027766017877 --mm --cp-ival 1 --cp-min 9 --np 2 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 892s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 892s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 892s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '2' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 892s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '7' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 892s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '8' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 892s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '11' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 892s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '18' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 892s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '21' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 892s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '22' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 892s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '24' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 892s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '28' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 892s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 892s Warning: skipping read '37' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 892s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '39' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 892s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '40' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 892s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '53' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 892s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '54' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 892s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '58' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 892s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '60' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 892s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '61' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 892s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '67' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 892s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '71' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 892s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '76' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 892s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '81' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 892s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '82' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 892s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '83' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 892s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '92' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 892s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '94' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 892s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '103' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 892s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '108' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 892s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '111' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 892s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '114' because it was < 2 characters long 892s 114 reads; of these: 892s 114 (100.00%) were unpaired; of these: 892s 103 (90.35%) aligned 0 times 892s 8 (7.02%) aligned exactly 1 time 892s 3 (2.63%) aligned >1 times 892s 9.65% overall alignment rate 892s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 892s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 892s /usr/bin/bowtie2 --ma 16.5983141483072 --score-min L,4.2534914545467,1.04027453922822 --rdg 27.8064912918731 --trim3 8 --rfg 24.5493053447879,16.1027766017877 --mm --cp-ival 1 --cp-min 9 --np 2 -f -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 892s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 892s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 892s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '2' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 892s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '7' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 892s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '8' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 892s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 892s Warning: skipping read '11' because it was < 2 characters long 892s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 892s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 893s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '18' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 893s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '21' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 893s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '22' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 893s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '24' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 893s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 893s Warning: skipping read '37' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 893s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '39' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 893s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '40' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 893s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '28' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 893s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '67' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 893s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '71' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 893s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '81' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 893s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '82' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 893s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '83' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 893s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '53' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 893s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '54' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 893s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '58' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 893s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '92' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 893s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '94' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 893s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '114' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 893s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '76' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 893s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '60' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 893s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '61' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 893s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '103' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 893s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '108' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 893s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '111' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 893s 114 reads; of these: 893s 114 (100.00%) were unpaired; of these: 893s 103 (90.35%) aligned 0 times 893s 8 (7.02%) aligned exactly 1 time 893s 3 (2.63%) aligned >1 times 893s 9.65% overall alignment rate 893s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 893s Flattened IUPAC characters 893s Mutating sequence Sim.pm.2 893s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 893s Finished SNPs 893s Finished ref gaps 893s Finished read gaps 893s Mutating sequence Sim.pm.1 893s Introducing 1 SNPs, 0/0 ref/read gaps, and 2 rearrangements 893s Finished SNPs 893s Finished ref gaps 893s Finished read gaps 893s Mutated reference genome to subject genome 893s SNPs introduced: 11 893s Reference gaps introduced: 0 893s Read gaps introduced: 0 893s Rearrangements introduced: 3 893s Created read sampler 893s Sampling 74 reads 893s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 893s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 893s parsing sequence Sim.pm.1... 893s parsing sequence Sim.pm.2... 893s Parsed 74 reference bases 893s *** Run 26 of 100 893s /usr/bin/bowtie2 --local --mp 6.9426656943404,4.80803255349527 --trim3 1 --rdg 26.4988386018208 --cp-min 3 --cp-ival 2 --mm --score-min L,7.35175285995891,1.83702074789757 -R 2 -D 30 -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 893s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '0' because it was < 2 characters long 893s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '5' because it was < 2 characters long 893s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '41' because it was < 2 characters long 893s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '46' because it was < 2 characters long 893s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 893s Warning: skipping read '68' because it was < 2 characters long 893s 74 reads; of these: 893s 74 (100.00%) were unpaired; of these: 893s 74 (100.00%) aligned 0 times 893s 0 (0.00%) aligned exactly 1 time 893s 0 (0.00%) aligned >1 times 893s 0.00% overall alignment rate 893s Read 50 alignments... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s --- Summary --- 893s Read 1 reference strings 893s Checked 0 alignments, 0 edits 893s --------------- 893s PASSED 893s ALSO checking that bowtie2 and bowtie2-align match up 893s /usr/bin/bowtie2 --local --mp 6.9426656943404,4.80803255349527 --trim3 1 --rdg 26.4988386018208 --cp-min 3 --cp-ival 2 --mm --score-min L,7.35175285995891,1.83702074789757 -R 2 -D 30 -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 893s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '0' because it was < 2 characters long 893s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '5' because it was < 2 characters long 893s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '41' because it was < 2 characters long 893s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 893s Warning: skipping read '46' because it was < 2 characters long 893s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 893s Warning: skipping read '68' because it was < 2 characters long 893s 74 reads; of these: 893s 74 (100.00%) were unpaired; of these: 893s 74 (100.00%) aligned 0 times 893s 0 (0.00%) aligned exactly 1 time 893s 0 (0.00%) aligned >1 times 893s 0.00% overall alignment rate 893s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 893s Flattened IUPAC characters 893s Mutating sequence Sim.pm.1 893s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 893s Finished SNPs 893s Finished ref gaps 893s Finished read gaps 893s Mutating sequence Sim.pm.2 893s Introducing 12 SNPs, 1/0 ref/read gaps, and 1 rearrangements 893s Finished SNPs 893s Finished ref gaps 893s Finished read gaps 893s Mutated reference genome to subject genome 893s SNPs introduced: 16 893s Reference gaps introduced: 1 893s Read gaps introduced: 0 893s Rearrangements introduced: 2 893s Created read sampler 893s Sampling 70 reads 893s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 893s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 893s parsing sequence Sim.pm.1... 893s parsing sequence Sim.pm.2... 893s Parsed 74 reference bases 893s *** Run 27 of 100 893s /usr/bin/bowtie2 --rdg 33.1452458912255 --rfg 36.6386572044743,8.83634336902257 --score-min L,3.74360533207956,7.69915139089705 --cp-min 2 --np 3 -N 0 -L14 --cp-ival 1 --mm -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 893s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 893s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 893s Warning: skipping read '20' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 893s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 893s Warning: skipping read '66' because it was < 2 characters long 893s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 893s 70 reads; of these: 893s 70 (100.00%) were unpaired; of these: 893s 62 (88.57%) aligned 0 times 893s 4 (5.71%) aligned exactly 1 time 893s 4 (5.71%) aligned >1 times 893s 11.43% overall alignment rate 893s Read 50 alignments... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s AA 893s AA 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s AC 893s AC 893s Processing line... 893s Processing line... 893s CTTTACACA 893s CTTTACACA 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s AAGGG 893s AAGGG 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s TAA 893s TAA 893s Processing line... 893s Processing line... 893s GGCGGGGT 893s GGCGGGGT 893s Processing line... 893s TAA 893s TAA 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s TGTACATGACTCTTTACACAAAGAG 893s TGTACATGACTCTTTACACAAAGAG 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s Processing line... 893s --- Summary --- 893s Read 1 reference strings 893s Checked 8 alignments, 0 edits 893s --------------- 893s PASSED 893s ALSO checking that bowtie2 and bowtie2-align match up 893s /usr/bin/bowtie2 --rdg 33.1452458912255 --rfg 36.6386572044743,8.83634336902257 --score-min L,3.74360533207956,7.69915139089705 --cp-min 2 --np 3 -N 0 -L14 --cp-ival 1 --mm -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 893s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 893s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 894s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 894s Warning: skipping read '20' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 894s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 894s Warning: skipping read '66' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 894s 70 reads; of these: 894s 70 (100.00%) were unpaired; of these: 894s 62 (88.57%) aligned 0 times 894s 4 (5.71%) aligned exactly 1 time 894s 4 (5.71%) aligned >1 times 894s 11.43% overall alignment rate 894s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 894s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 894s /usr/bin/bowtie2 --rdg 33.1452458912255 --rfg 36.6386572044743,8.83634336902257 --score-min L,3.74360533207956,7.69915139089705 --cp-min 2 --np 3 -N 0 -L14 --cp-ival 1 --mm -r -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 894s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 894s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 894s Warning: skipping read '20' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 894s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 894s Warning: skipping read '66' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 894s 70 reads; of these: 894s 70 (100.00%) were unpaired; of these: 894s 62 (88.57%) aligned 0 times 894s 4 (5.71%) aligned exactly 1 time 894s 4 (5.71%) aligned >1 times 894s 11.43% overall alignment rate 894s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 894s Flattened IUPAC characters 894s Mutating sequence Sim.pm.1 894s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 894s Finished SNPs 894s Finished ref gaps 894s Finished read gaps 894s Mutating sequence Sim.pm.2 894s Introducing 9 SNPs, 0/1 ref/read gaps, and 0 rearrangements 894s Finished SNPs 894s Finished ref gaps 894s Finished read gaps 894s Mutated reference genome to subject genome 894s SNPs introduced: 15 894s Reference gaps introduced: 1 894s Read gaps introduced: 1 894s Rearrangements introduced: 0 894s Created read sampler 894s Sampling 71 reads 894s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 894s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 894s parsing sequence Sim.pm.1... 894s parsing sequence Sim.pm.2... 894s Parsed 74 reference bases 894s *** Run 28 of 100 894s /usr/bin/bowtie2 --rfg 37.7871286565931 -i C --trim5 8 --score-min L,6.66379131163576,5.39324854008207 --np 3 --rdg 12.3670013822592,10.8777042094641 --mp 8.32719430272073,5.56356018590863 --ma 30.6143293609926 --cp-min 5 --cp-ival 1 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 894s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 894s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 894s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '2' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 894s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 894s Warning: skipping read '3' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 894s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '10' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 894s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '13' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 894s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 894s Warning: skipping read '14' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 894s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '24' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 894s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '29' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 894s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '31' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 894s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '32' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 894s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '41' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 894s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '46' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 894s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '47' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 894s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '52' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 894s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '53' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 894s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '56' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 894s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '63' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 894s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '68' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 894s 71 reads; of these: 894s 71 (100.00%) were unpaired; of these: 894s 59 (83.10%) aligned 0 times 894s 7 (9.86%) aligned exactly 1 time 894s 5 (7.04%) aligned >1 times 894s 16.90% overall alignment rate 894s Read 50 alignments... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s TGACTCTTTACACAAA 894s TGACTCTTTACACAAA 894s Processing line... 894s Processing line... 894s Processing line... 894s GCG 894s GCG 894s Processing line... 894s Processing line... 894s TCTTTACACAAAGAGGCG 894s TCTTTACACAAAGAGGCG 894s Processing line... 894s TT 894s TT 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s ATT 894s ATT 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s CATGACTCTTTACACAAAGAG 894s CATGACTCTTTACACAAAGAG 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s CATGACTCTTTACACA 894s CATGACTCTTTACACA 894s Processing line... 894s /usr/bin/bowtie2 --rfg 37.7871286565931 -i C --trim5 8 --score-min L,6.66379131163576,5.39324854008207 --np 3 --rdg 12.3670013822592,10.8777042094641 --mp 8.32719430272073,5.56356018590863 --ma 30.6143293609926 --cp-min 5 --cp-ival 1 -q -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 894s Processing line... 894s Processing line... 894s Processing line... 894s GGA 894s GGA 894s Processing line... 894s Processing line... 894s TA 894s TA 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s CTCTT 894s CTCTT 894s Processing line... 894s AT 894s AT 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s Processing line... 894s AAAGAGG 894s AAAGAGG 894s Processing line... 894s Processing line... 894s --- Summary --- 894s Read 1 reference strings 894s Checked 12 alignments, 0 edits 894s --------------- 894s PASSED 894s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 894s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 894s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 894s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 894s Warning: skipping read '2' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 894s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 894s Warning: skipping read '3' because it was < 2 characters long 894s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 894s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 895s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '10' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 895s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '13' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 895s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 895s Warning: skipping read '14' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 895s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '52' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 895s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '53' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 895s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '56' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 895s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '24' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 895s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '68' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 895s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '63' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 895s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '29' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 895s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '31' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 895s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '32' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 895s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '41' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 895s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '46' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 895s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '47' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 895s 71 reads; of these: 895s 71 (100.00%) were unpaired; of these: 895s 59 (83.10%) aligned 0 times 895s 7 (9.86%) aligned exactly 1 time 895s 5 (7.04%) aligned >1 times 895s 16.90% overall alignment rate 895s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 895s Flattened IUPAC characters 895s Mutating sequence Sim.pm.2 895s Introducing 1 SNPs, 0/3 ref/read gaps, and 0 rearrangements 895s Finished SNPs 895s Finished ref gaps 895s Finished read gaps 895s Mutating sequence Sim.pm.1 895s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 895s Finished SNPs 895s Finished ref gaps 895s Finished read gaps 895s Mutated reference genome to subject genome 895s SNPs introduced: 10 895s Reference gaps introduced: 0 895s Read gaps introduced: 3 895s Rearrangements introduced: 0 895s Created read sampler 895s Sampling 52 reads 895s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 895s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 895s parsing sequence Sim.pm.1... 895s parsing sequence Sim.pm.2... 895s *** Run 29 of 100 895s /usr/bin/bowtie2 --mp 9.10959070516527,4.84226487185458 --trim5 8 --score-min L,4.34180181522535,6.05646208664369 -k 6 --cp-min 4 -R 4 --cp-ival 1 -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw 895s Parsed 74 reference bases 895s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 895s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '1' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 895s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '2' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 895s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 895s Warning: skipping read '11' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 895s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '18' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 895s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '22' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 895s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 895s Warning: skipping read '26' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 895s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '31' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 895s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '33' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 895s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '36' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 895s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '41' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 895s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '43' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 895s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '48' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 895s 52 reads; of these: 895s 37 (71.15%) were paired; of these: 895s 36 (97.30%) aligned concordantly 0 times 895s 0 (0.00%) aligned concordantly exactly 1 time 895s 1 (2.70%) aligned concordantly >1 times 895s ---- 895s 36 pairs aligned concordantly 0 times; of these: 895s 1 (2.78%) aligned discordantly 1 time 895s ---- 895s 35 pairs aligned 0 times concordantly or discordantly; of these: 895s 70 mates make up the pairs; of these: 895s 61 (87.14%) aligned 0 times 895s 5 (7.14%) aligned exactly 1 time 895s 4 (5.71%) aligned >1 times 895s 15 (28.85%) were unpaired; of these: 895s 12 (80.00%) aligned 0 times 895s 0 (0.00%) aligned exactly 1 time 895s 3 (20.00%) aligned >1 times 895s 17.98% overall alignment rate 895s Read 50 alignments... 895s Read 100 alignments... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s AC 895s AC 895s Processing line... 895s AC 895s AC 895s Processing line... 895s AC 895s AC 895s Processing line... 895s AC 895s AC 895s Processing line... 895s AC 895s AC 895s Processing line... 895s AC 895s AC 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s ACATGACTCTTTACACAAA 895s ACATGACTCTTTACACAAA 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s CAAAGAGGCGGGGTAACATTCAGCTACCA 895s CAAAGAGGCGGGGTAACATTCAGCTACCA 895s Processing line... 895s Processing line... 895s Processing line... 895s TTACACAAA 895s TTACACAAA 895s Processing line... 895s ACTCTTTACACAAAGAGGCGGGGTAA 895s ACTCTTTACACAAAGAGGCGGGGTAA 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s CGGGGTA 895s CGGGGTA 895s Processing line... 895s Processing line... 895s TACA 895s TACA 895s Processing line... 895s TACA 895s TACA 895s Processing line... 895s TGTA 895s TGTA 895s Processing line... 895s Processing line... 895s AC 895s AC 895s Processing line... 895s AC 895s AC 895s Processing line... 895s AC 895s AC 895s Processing line... 895s AC 895s AC 895s Processing line... 895s AC 895s AC 895s Processing line... 895s AC 895s AC 895s Processing line... 895s Processing line... 895s GGG 895s GGG 895s Processing line... 895s GGG 895s GGG 895s Processing line... 895s GGG 895s GGG 895s Processing line... 895s GGG 895s GGG 895s Processing line... 895s GGG 895s GGG 895s Processing line... 895s GG 895s GG 895s Processing line... 895s GG 895s GG 895s Processing line... 895s GG 895s GG 895s Processing line... 895s GG 895s GG 895s Processing line... 895s GG 895s GG 895s Processing line... 895s GG 895s GG 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s TCTTTACACAAAGAGGCGGGGTAAC 895s TCTTTACACAAAGAGGCGGGGTAAC 895s Processing line... 895s Processing line... 895s ACAAAGAGGCGGGGTAAC 895s ACAAAGAGGCGGGGTAAC 895s Processing line... 895s Processing line... 895s GGGTAACA 895s GGGTAACA 895s Processing line... 895s AA 895s AA 895s Processing line... 895s GGGTAACA 895s GGGTAACA 895s Processing line... 895s AA 895s AA 895s Processing line... 895s TCA 895s TCA 895s Processing line... 895s TGA 895s TGA 895s Processing line... 895s GCT 895s GCT 895s Processing line... 895s AGC 895s AGC 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s Processing line... 895s --- Summary --- 895s Read 1 reference strings 895s Checked 41 alignments, 0 edits 895s --------------- 895s PASSED 895s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 895s /usr/bin/bowtie2 --mp 9.10959070516527,4.84226487185458 --trim5 8 --score-min L,4.34180181522535,6.05646208664369 -k 6 --cp-min 4 -R 4 --cp-ival 1 -r -p 4 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 895s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 895s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '1' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 895s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '2' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 895s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '33' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 895s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 895s Warning: skipping read '11' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 895s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '48' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 895s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '18' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 895s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '22' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 895s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '36' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 895s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 895s Warning: skipping read '26' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 895s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 895s Warning: skipping read '31' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 895s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '41' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 895s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 895s Warning: skipping mate #1 of read '43' because it was < 2 characters long 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 895s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 895s 52 reads; of these: 895s 37 (71.15%) were paired; of these: 895s 36 (97.30%) aligned concordantly 0 times 895s 0 (0.00%) aligned concordantly exactly 1 time 895s 1 (2.70%) aligned concordantly >1 times 895s ---- 895s 36 pairs aligned concordantly 0 times; of these: 895s 1 (2.78%) aligned discordantly 1 time 895s ---- 895s 35 pairs aligned 0 times concordantly or discordantly; of these: 895s 70 mates make up the pairs; of these: 895s 61 (87.14%) aligned 0 times 895s 5 (7.14%) aligned exactly 1 time 895s 4 (5.71%) aligned >1 times 895s 15 (28.85%) were unpaired; of these: 895s 12 (80.00%) aligned 0 times 895s 0 (0.00%) aligned exactly 1 time 895s 3 (20.00%) aligned >1 times 895s 17.98% overall alignment rate 895s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 895s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 895s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 895s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 895s /usr/bin/bowtie2 --mp 9.10959070516527,4.84226487185458 --trim5 8 --score-min L,4.34180181522535,6.05646208664369 -k 6 --cp-min 4 -R 4 --cp-ival 1 -r -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 896s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 896s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '1' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 896s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '2' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 896s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '33' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 896s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 896s Warning: skipping read '11' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 896s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '18' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 896s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '48' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 896s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '22' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 896s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 896s Warning: skipping read '26' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 896s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '36' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 896s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '41' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 896s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '43' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 896s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '31' because it was < 2 characters long 896s 52 reads; of these: 896s 37 (71.15%) were paired; of these: 896s 36 (97.30%) aligned concordantly 0 times 896s 0 (0.00%) aligned concordantly exactly 1 time 896s 1 (2.70%) aligned concordantly >1 times 896s ---- 896s 36 pairs aligned concordantly 0 times; of these: 896s 1 (2.78%) aligned discordantly 1 time 896s ---- 896s 35 pairs aligned 0 times concordantly or discordantly; of these: 896s 70 mates make up the pairs; of these: 896s 61 (87.14%) aligned 0 times 896s 5 (7.14%) aligned exactly 1 time 896s 4 (5.71%) aligned >1 times 896s 15 (28.85%) were unpaired; of these: 896s 12 (80.00%) aligned 0 times 896s 0 (0.00%) aligned exactly 1 time 896s 3 (20.00%) aligned >1 times 896s 17.98% overall alignment rate 896s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 896s Flattened IUPAC characters 896s Mutating sequence Sim.pm.2 896s Introducing 8 SNPs, 1/1 ref/read gaps, and 0 rearrangements 896s Finished SNPs 896s Finished ref gaps 896s Finished read gaps 896s Mutating sequence Sim.pm.1 896s Introducing 6 SNPs, 0/0 ref/read gaps, and 2 rearrangements 896s Finished SNPs 896s Finished ref gaps 896s Finished read gaps 896s Mutated reference genome to subject genome 896s SNPs introduced: 14 896s Reference gaps introduced: 1 896s Read gaps introduced: 1 896s Rearrangements introduced: 2 896s Created read sampler 896s Sampling 101 reads 896s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 896s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 896s parsing sequence Sim.pm.1... 896s parsing sequence Sim.pm.2... 896s Parsed 74 reference bases 896s *** Run 30 of 100 896s /usr/bin/bowtie2 --local --trim3 8 --mp 7.96319855929906,1.85709378488966 --rdg 8.90478221322712 -k 13 --cp-min 2 --cp-ival 2 --mm --score-min L,1.98106886837206,7.67811959406369 --norc -R 2 -D 2 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 896s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '5' because it was < 2 characters long 896s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '8' because it was < 2 characters long 896s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '15' because it was < 2 characters long 896s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '19' because it was < 2 characters long 896s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '20' because it was < 2 characters long 896s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '24' because it was < 2 characters long 896s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '26' because it was < 2 characters long 896s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '31' because it was < 2 characters long 896s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '42' because it was < 2 characters long 896s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '53' because it was < 2 characters long 896s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '59' because it was < 2 characters long 896s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 896s Warning: skipping mate #2 of read '61' because it was < 2 characters long 896s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '63' because it was < 2 characters long 896s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '66' because it was < 2 characters long 896s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '69' because it was < 2 characters long 896s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '79' because it was < 2 characters long 896s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '80' because it was < 2 characters long 896s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '84' because it was < 2 characters long 896s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '89' because it was < 2 characters long 896s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '90' because it was < 2 characters long 896s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '95' because it was < 2 characters long 896s Read 50 alignments... 896s 101 reads; of these: 896s 85 (84.16%) were paired; of these: 896s 85 (100.00%) aligned concordantly 0 times 896s 0 (0.00%) aligned concordantly exactly 1 time 896s 0 (0.00%) aligned concordantly >1 times 896s ---- 896s 85 pairs aligned concordantly 0 times; of these: 896s 0 (0.00%) aligned discordantly 1 time 896s ---- 896s 85 pairs aligned 0 times concordantly or discordantly; of these: 896s 170 mates make up the pairs; of these: 896s 170 (100.00%) aligned 0 times 896s 0 (0.00%) aligned exactly 1 time 896s 0 (0.00%) aligned >1 times 896s 16 (15.84%) were unpaired; of these: 896s 16 (100.00%) aligned 0 times 896s 0 (0.00%) aligned exactly 1 time 896s 0 (0.00%) aligned >1 times 896s 0.00% overall alignment rate 896s Read 100 alignments... 896s Read 150 alignments... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s --- Summary --- 896s Read 1 reference strings 896s Checked 0 alignments, 0 edits 896s --------------- 896s PASSED 896s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 896s /usr/bin/bowtie2 --local --trim3 8 --mp 7.96319855929906,1.85709378488966 --rdg 8.90478221322712 -k 13 --cp-min 2 --cp-ival 2 --mm --score-min L,1.98106886837206,7.67811959406369 --norc -R 2 -D 2 -q -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 896s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '5' because it was < 2 characters long 896s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '8' because it was < 2 characters long 896s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '15' because it was < 2 characters long 896s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '42' because it was < 2 characters long 896s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '19' because it was < 2 characters long 896s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '20' because it was < 2 characters long 896s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '24' because it was < 2 characters long 896s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '26' because it was < 2 characters long 896s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '31' because it was < 2 characters long 896s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '53' because it was < 2 characters long 896s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '59' because it was < 2 characters long 896s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 896s Warning: skipping mate #2 of read '61' because it was < 2 characters long 896s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '63' because it was < 2 characters long 896s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '66' because it was < 2 characters long 896s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '69' because it was < 2 characters long 896s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '79' because it was < 2 characters long 896s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '80' because it was < 2 characters long 896s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '84' because it was < 2 characters long 896s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '89' because it was < 2 characters long 896s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '90' because it was < 2 characters long 896s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 896s Warning: skipping mate #1 of read '95' because it was < 2 characters long 896s 101 reads; of these: 896s 85 (84.16%) were paired; of these: 896s 85 (100.00%) aligned concordantly 0 times 896s 0 (0.00%) aligned concordantly exactly 1 time 896s 0 (0.00%) aligned concordantly >1 times 896s ---- 896s 85 pairs aligned concordantly 0 times; of these: 896s 0 (0.00%) aligned discordantly 1 time 896s ---- 896s 85 pairs aligned 0 times concordantly or discordantly; of these: 896s 170 mates make up the pairs; of these: 896s 170 (100.00%) aligned 0 times 896s 0 (0.00%) aligned exactly 1 time 896s 0 (0.00%) aligned >1 times 896s 16 (15.84%) were unpaired; of these: 896s 16 (100.00%) aligned 0 times 896s 0 (0.00%) aligned exactly 1 time 896s 0 (0.00%) aligned >1 times 896s 0.00% overall alignment rate 896s Flattened IUPAC characters 896s Mutating sequence Sim.pm.1 896s Introducing 10 SNPs, 0/2 ref/read gaps, and 0 rearrangements 896s Finished SNPs 896s Finished ref gaps 896s Finished read gaps 896s Mutating sequence Sim.pm.2 896s Introducing 9 SNPs, 0/1 ref/read gaps, and 3 rearrangements 896s Finished SNPs 896s Finished ref gaps 896s Finished read gaps 896s Mutated reference genome to subject genome 896s SNPs introduced: 19 896s Reference gaps introduced: 0 896s Read gaps introduced: 3 896s Rearrangements introduced: 3 896s Created read sampler 896s Sampling 68 reads 896s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 896s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 896s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 896s parsing sequence Sim.pm.1... 896s parsing sequence Sim.pm.2... 896s Parsed 74 reference bases 896s *** Run 31 of 100 896s /usr/bin/bowtie2 -R 4 --nofw --np 8 --score-min L,7.74213698137628,6.00350195555839 --trim5 8 --cp-ival 2 --mm --cp-min 6 --ma 31.516613171395 -M 4 --rdg 29.9089748329776,3.70077819776076 -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 896s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 896s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 896s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 896s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '0' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 896s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '3' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 896s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '4' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 896s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '5' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 896s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '6' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 896s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '7' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 896s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '10' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 896s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '11' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 896s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '15' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 896s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '18' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 896s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '20' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 896s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '22' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 896s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '26' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 896s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '27' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 896s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '33' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 896s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '46' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 896s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 896s Warning: skipping read '51' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 896s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '52' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 896s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 896s Warning: skipping read '61' because it was < 2 characters long 896s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 896s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 896s 68 reads; of these: 896s 68 (100.00%) were unpaired; of these: 896s 67 (98.53%) aligned 0 times 896s 1 (1.47%) aligned exactly 1 time 896s 0 (0.00%) aligned >1 times 896s 1.47% overall alignment rate 896s Read 50 alignments... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s AGGC 896s AGGC 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s Processing line... 896s --- Summary --- 896s Read 1 reference strings 896s Checked 1 alignments, 0 edits 896s --------------- 896s PASSED 896s Flattened IUPAC characters 896s Mutating sequence Sim.pm.2 896s Introducing 6 SNPs, 2/2 ref/read gaps, and 1 rearrangements 896s Finished SNPs 896s Finished ref gaps 896s Finished read gaps 896s Mutating sequence Sim.pm.1 896s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 896s Finished SNPs 896s Finished ref gaps 896s Finished read gaps 896s Mutated reference genome to subject genome 896s SNPs introduced: 8 896s Reference gaps introduced: 2 896s Read gaps introduced: 3 896s Rearrangements introduced: 1 896s Created read sampler 896s Sampling 70 reads 896s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 896s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 896s parsing sequence Sim.pm.1... 897s parsing sequence Sim.pm.2... 897s Parsed 74 reference bases 897s *** Run 32 of 100 897s /usr/bin/bowtie2 --cp-min 5 --cp-ival 1 --mm --local --trim3 0 --np 11 --norc --trim5 3 --score-min L,5.39371409195741,9.31117584903257 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 897s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 897s Warning: skipping mate #1 of read '26' because it was < 2 characters long 897s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 897s Warning: skipping mate #2 of read '59' because it was < 2 characters long 897s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 897s Warning: skipping mate #1 of read '63' because it was < 2 characters long 897s Read 50 alignments... 897s 70 reads; of these: 897s 66 (94.29%) were paired; of these: 897s 66 (100.00%) aligned concordantly 0 times 897s 0 (0.00%) aligned concordantly exactly 1 time 897s 0 (0.00%) aligned concordantly >1 times 897s ---- 897s 66 pairs aligned concordantly 0 times; of these: 897s 0 (0.00%) aligned discordantly 1 time 897s ---- 897s 66 pairs aligned 0 times concordantly or discordantly; of these: 897s 132 mates make up the pairs; of these: 897s 132 (100.00%) aligned 0 times 897s 0 (0.00%) aligned exactly 1 time 897s 0 (0.00%) aligned >1 times 897s 4 (5.71%) were unpaired; of these: 897s 4 (100.00%) aligned 0 times 897s 0 (0.00%) aligned exactly 1 time 897s 0 (0.00%) aligned >1 times 897s 0.00% overall alignment rate 897s Read 100 alignments... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s --- Summary --- 897s Read 1 reference strings 897s Checked 0 alignments, 0 edits 897s --------------- 897s PASSED 897s ALSO checking that bowtie2 and bowtie2-align match up 897s /usr/bin/bowtie2 --cp-min 5 --cp-ival 1 --mm --local --trim3 0 --np 11 --norc --trim5 3 --score-min L,5.39371409195741,9.31117584903257 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 897s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 897s Warning: skipping mate #1 of read '26' because it was < 2 characters long 897s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 897s Warning: skipping mate #2 of read '59' because it was < 2 characters long 897s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 897s Warning: skipping mate #1 of read '63' because it was < 2 characters long 897s 70 reads; of these: 897s 66 (94.29%) were paired; of these: 897s 66 (100.00%) aligned concordantly 0 times 897s 0 (0.00%) aligned concordantly exactly 1 time 897s 0 (0.00%) aligned concordantly >1 times 897s ---- 897s 66 pairs aligned concordantly 0 times; of these: 897s 0 (0.00%) aligned discordantly 1 time 897s ---- 897s 66 pairs aligned 0 times concordantly or discordantly; of these: 897s 132 mates make up the pairs; of these: 897s 132 (100.00%) aligned 0 times 897s 0 (0.00%) aligned exactly 1 time 897s 0 (0.00%) aligned >1 times 897s 4 (5.71%) were unpaired; of these: 897s 4 (100.00%) aligned 0 times 897s 0 (0.00%) aligned exactly 1 time 897s 0 (0.00%) aligned >1 times 897s 0.00% overall alignment rate 897s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 897s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 897s /usr/bin/bowtie2 --cp-min 5 --cp-ival 1 --mm --local --trim3 0 --np 11 --norc --trim5 3 --score-min L,5.39371409195741,9.31117584903257 -q -p 2 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 897s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 897s Warning: skipping mate #1 of read '26' because it was < 2 characters long 897s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 897s Warning: skipping mate #2 of read '59' because it was < 2 characters long 897s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 897s Warning: skipping mate #1 of read '63' because it was < 2 characters long 897s 70 reads; of these: 897s 66 (94.29%) were paired; of these: 897s 66 (100.00%) aligned concordantly 0 times 897s 0 (0.00%) aligned concordantly exactly 1 time 897s 0 (0.00%) aligned concordantly >1 times 897s ---- 897s 66 pairs aligned concordantly 0 times; of these: 897s 0 (0.00%) aligned discordantly 1 time 897s ---- 897s 66 pairs aligned 0 times concordantly or discordantly; of these: 897s 132 mates make up the pairs; of these: 897s 132 (100.00%) aligned 0 times 897s 0 (0.00%) aligned exactly 1 time 897s 0 (0.00%) aligned >1 times 897s 4 (5.71%) were unpaired; of these: 897s 4 (100.00%) aligned 0 times 897s 0 (0.00%) aligned exactly 1 time 897s 0 (0.00%) aligned >1 times 897s 0.00% overall alignment rate 897s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 897s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 897s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 897s Flattened IUPAC characters 897s Mutating sequence Sim.pm.1 897s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 897s Finished SNPs 897s Finished ref gaps 897s Finished read gaps 897s Mutating sequence Sim.pm.2 897s Introducing 12 SNPs, 1/0 ref/read gaps, and 4 rearrangements 897s Finished SNPs 897s Finished ref gaps 897s Finished read gaps 897s Mutated reference genome to subject genome 897s SNPs introduced: 12 897s Reference gaps introduced: 1 897s Read gaps introduced: 1 897s Rearrangements introduced: 4 897s Created read sampler 897s Sampling 52 reads 897s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 897s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 897s parsing sequence Sim.pm.1... 897s parsing sequence Sim.pm.2... 897s Parsed 74 reference bases 897s *** Run 33 of 100 897s /usr/bin/bowtie2 --trim3 1 --mp 9.75796793048609,2.98248546966876 -a --trim5 1 --score-min L,1.47298980467214,4.10249424572662 --gbar 1 --cp-min 3 --cp-ival 2 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 897s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 897s Warning: skipping mate #1 of read '2' because it was < 2 characters long 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 897s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 897s Warning: skipping mate #2 of read '41' because it was < 2 characters long 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 897s Read 50 alignments... 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 897s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 897s 52 reads; of these: 897s 47 (90.38%) were paired; of these: 897s 47 (100.00%) aligned concordantly 0 times 897s 0 (0.00%) aligned concordantly exactly 1 time 897s 0 (0.00%) aligned concordantly >1 times 897s ---- 897s 47 pairs aligned concordantly 0 times; of these: 897s 0 (0.00%) aligned discordantly 1 time 897s ---- 897s 47 pairs aligned 0 times concordantly or discordantly; of these: 897s 94 mates make up the pairs; of these: 897s 81 (86.17%) aligned 0 times 897s 8 (8.51%) aligned exactly 1 time 897s 5 (5.32%) aligned >1 times 897s 5 (9.62%) were unpaired; of these: 897s 5 (100.00%) aligned 0 times 897s 0 (0.00%) aligned exactly 1 time 897s 0 (0.00%) aligned >1 times 897s 13.13% overall alignment rate 897s Read 100 alignments... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s TTTACACA 897s TTTACACA 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s TGACTCTTTACACAAA 897s TGACTCTTTACACAAA 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s GGTA 897s GGTA 897s Processing line... 897s TACC 897s TACC 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s AGC 897s AGC 897s Processing line... 897s GCT 897s GCT 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s AGA 897s AGA 897s Processing line... 897s TCT 897s TCT 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s AGCTAC 897s AGCTAC 897s Processing line... 897s Processing line... 897s Processing line... 897s CACAAAGAG 897s CACAAAGAG 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s TCTTTACACAA 897s TCTTTACACAA 897s Processing line... 897s Processing line... 897s GGG 897s GGG 897s Processing line... 897s GGG 897s GGG 897s Processing line... 897s GGG 897s GGG 897s Processing line... 897s GGG 897s GGG 897s Processing line... 897s GGG 897s GGG 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s ACAAAGAGGCGG 897s ACAAAGAGGCGG 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s GCT 897s GCT 897s Processing line... 897s AGC 897s AGC 897s Processing line... 897s /usr/bin/bowtie2 --trim3 1 --mp 9.75796793048609,2.98248546966876 -a --trim5 1 --score-min L,1.47298980467214,4.10249424572662 --gbar 1 --cp-min 3 --cp-ival 2 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 897s Processing line... 897s GGAG 897s GGAG 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s ACATTCAGCTA 897s ACATTCAGCTA 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s Processing line... 897s --- Summary --- 897s Read 1 reference strings 897s Checked 21 alignments, 0 edits 897s --------------- 897s PASSED 897s ALSO checking that bowtie2 and bowtie2-align match up 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 898s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '2' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 898s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 898s Warning: skipping mate #2 of read '41' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 898s 52 reads; of these: 898s 47 (90.38%) were paired; of these: 898s 47 (100.00%) aligned concordantly 0 times 898s 0 (0.00%) aligned concordantly exactly 1 time 898s 0 (0.00%) aligned concordantly >1 times 898s ---- 898s 47 pairs aligned concordantly 0 times; of these: 898s 0 (0.00%) aligned discordantly 1 time 898s ---- 898s 47 pairs aligned 0 times concordantly or discordantly; of these: 898s 94 mates make up the pairs; of these: 898s 81 (86.17%) aligned 0 times 898s 8 (8.51%) aligned exactly 1 time 898s 5 (5.32%) aligned >1 times 898s 5 (9.62%) were unpaired; of these: 898s 5 (100.00%) aligned 0 times 898s 0 (0.00%) aligned exactly 1 time 898s 0 (0.00%) aligned >1 times 898s 13.13% overall alignment rate 898s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 898s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 898s /usr/bin/bowtie2 --trim3 1 --mp 9.75796793048609,2.98248546966876 -a --trim5 1 --score-min L,1.47298980467214,4.10249424572662 --gbar 1 --cp-min 3 --cp-ival 2 -q -p 3 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 898s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '2' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 898s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 898s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 898s Warning: skipping mate #2 of read '41' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 898s 52 reads; of these: 898s 47 (90.38%) were paired; of these: 898s 47 (100.00%) aligned concordantly 0 times 898s 0 (0.00%) aligned concordantly exactly 1 time 898s 0 (0.00%) aligned concordantly >1 times 898s ---- 898s 47 pairs aligned concordantly 0 times; of these: 898s 0 (0.00%) aligned discordantly 1 time 898s ---- 898s 47 pairs aligned 0 times concordantly or discordantly; of these: 898s 94 mates make up the pairs; of these: 898s 81 (86.17%) aligned 0 times 898s 8 (8.51%) aligned exactly 1 time 898s 5 (5.32%) aligned >1 times 898s 5 (9.62%) were unpaired; of these: 898s 5 (100.00%) aligned 0 times 898s 0 (0.00%) aligned exactly 1 time 898s 0 (0.00%) aligned >1 times 898s 13.13% overall alignment rate 898s Flattened IUPAC characters 898s Mutating sequence Sim.pm.1 898s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 898s Finished SNPs 898s Finished ref gaps 898s Finished read gaps 898s Mutating sequence Sim.pm.2 898s Introducing 12 SNPs, 0/0 ref/read gaps, and 3 rearrangements 898s Finished SNPs 898s Finished ref gaps 898s Finished read gaps 898s Mutated reference genome to subject genome 898s SNPs introduced: 18 898s Reference gaps introduced: 0 898s Read gaps introduced: 0 898s Rearrangements introduced: 3 898s Created read sampler 898s Sampling 152 reads 898s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 898s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 898s parsing sequence Sim.pm.1... 898s parsing sequence Sim.pm.2... 898s Parsed 74 reference bases 898s *** Run 34 of 100 898s /usr/bin/bowtie2 --trim5 8 --score-min L,7.32961241389488,3.68607732761492 --cp-min 8 --cp-ival 5 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 898s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 898s Warning: skipping read '11' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 898s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '12' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 898s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 898s Warning: skipping read '14' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 898s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '20' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 898s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '26' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 898s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '27' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 898s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '34' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 898s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '40' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 898s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '41' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 898s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '54' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 898s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 898s Warning: skipping read '58' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 898s Read 50 alignments... 898s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 898s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 898s Warning: skipping read '66' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 898s Read 100 alignments... 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 898s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 898s Warning: skipping read '72' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 898s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 898s Warning: skipping mate #2 of read '75' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 898s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '84' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 898s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '91' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 898s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '92' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 898s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '95' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 898s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '96' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 898s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '101' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 898s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '105' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 898s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '111' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 898s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 898s Warning: skipping read '113' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 898s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '116' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 898s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '127' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 898s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 898s Warning: skipping read '129' because it was < 2 characters long 898s Read 150 alignments... 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 898s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '140' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 898s Warning: skipping mate #1 of read '145' because length (1) <= # seed mismatches (0) 898s Warning: skipping mate #1 of read '145' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 898s Warning: skipping mate #2 of read '147' because length (1) <= # seed mismatches (0) 898s Warning: skipping mate #2 of read '147' because it was < 2 characters long 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 898s Read 200 alignments... 898s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 898s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 898s 152 reads; of these: 898s 126 (82.89%) were paired; of these: 898s 126 (100.00%) aligned concordantly 0 times 898s 0 (0.00%) aligned concordantly exactly 1 time 898s 0 (0.00%) aligned concordantly >1 times 898s ---- 898s 126 pairs aligned concordantly 0 times; of these: 898s 0 (0.00%) aligned discordantly 1 time 898s ---- 898s 126 pairs aligned 0 times concordantly or discordantly; of these: 898s 252 mates make up the pairs; of these: 898s 225 (89.29%) aligned 0 times 898s 16 (6.35%) aligned exactly 1 time 898s 11 (4.37%) aligned >1 times 898s 26 (17.11%) were unpaired; of these: 898s 23 (88.46%) aligned 0 times 898s 2 (7.69%) aligned exactly 1 time 898s 1 (3.85%) aligned >1 times 898s 10.79% overall alignment rate 898s Read 250 alignments... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s CGGG 898s CGGG 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s TTTA 898s TTTA 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s CGA 898s CGA 898s Processing line... 898s Processing line... 898s CAG 898s CAG 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s TGTACATG 898s TGTACATG 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s GCG 898s GCG 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s TCAGC 898s TCAGC 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s AAGA 898s AAGA 898s Processing line... 898s Processing line... 898s AGG 898s AGG 898s Processing line... 898s GGGGTAA 898s GGGGTAA 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s CATG 898s CATG 898s Processing line... 898s Processing line... 898s AAGGG 898s AAGGG 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s AGGCGGGGTAACAT 898s AGGCGGGGTAACAT 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s AAGAGGCGGG 898s AAGAGGCGGG 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s CGG 898s CGG 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s AA 898s AA 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s CGGGGTAACA 898s CGGGGTAACA 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s GCGGGGTAAC 898s GCGGGGTAAC 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s ATGACTCTTT 898s ATGACTCTTT 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s CTC 898s CTC 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s CTCT 898s CTCT 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s TACATGAC 898s TACATGAC 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s TTAC 898s TTAC 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s GGC 898s GGC 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s GTACATGACT 898s GTACATGACT 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s GACTCTTTA 898s GACTCTTTA 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s GA 898s GA 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s CGGG 898s CGGG 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s AAAGAGGCGG 898s AAAGAGGCGG 898s Processing line... 898s Processing line... 898s CACAAAGAGGCGGGGTAA 898s CACAAAGAGGCGGGGTAA 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s Processing line... 898s --- Summary --- 898s Read 1 reference strings 898s Checked 30 alignments, 0 edits 898s --------------- 898s PASSED 898s Flattened IUPAC characters 898s Mutating sequence Sim.pm.2 898s Introducing 6 SNPs, 2/2 ref/read gaps, and 1 rearrangements 898s Finished SNPs 898s Finished ref gaps 898s Finished read gaps 898s Mutating sequence Sim.pm.1 898s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 898s Finished SNPs 898s Finished ref gaps 898s Finished read gaps 898s Mutated reference genome to subject genome 898s SNPs introduced: 9 898s Reference gaps introduced: 2 898s Read gaps introduced: 3 898s Rearrangements introduced: 1 898s Created read sampler 898s Sampling 54 reads 898s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 898s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 898s parsing sequence Sim.pm.1... 898s parsing sequence Sim.pm.2... 898s Parsed 74 reference bases 898s *** Run 35 of 100 898s /usr/bin/bowtie2 --np 1 --norc -R 3 --n-ceil 1.2611343391223,0.944838868599061 --score-min L,9.1474068991512,8.53052820083448 --cp-min 2 --cp-ival 2 --mm --mp 9.06384054079021,4.11156881297163 --trim3 4 --local -M 4 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq 899s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 899s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 899s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 899s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 899s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 899s 54 reads; of these: 899s 50 (92.59%) were paired; of these: 899s 50 (100.00%) aligned concordantly 0 times 899s 0 (0.00%) aligned concordantly exactly 1 time 899s 0 (0.00%) aligned concordantly >1 times 899s ---- 899s 50 pairs aligned concordantly 0 times; of these: 899s 0 (0.00%) aligned discordantly 1 time 899s ---- 899s 50 pairs aligned 0 times concordantly or discordantly; of these: 899s 100 mates make up the pairs; of these: 899s 100 (100.00%) aligned 0 times 899s 0 (0.00%) aligned exactly 1 time 899s 0 (0.00%) aligned >1 times 899s 4 (7.41%) were unpaired; of these: 899s 4 (100.00%) aligned 0 times 899s 0 (0.00%) aligned exactly 1 time 899s 0 (0.00%) aligned >1 times 899s 0.00% overall alignment rate 899s Read 50 alignments... 899s Read 100 alignments... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s /usr/bin/bowtie2 --np 1 --norc -R 3 --n-ceil 1.2611343391223,0.944838868599061 --score-min L,9.1474068991512,8.53052820083448 --cp-min 2 --cp-ival 2 --mm --mp 9.06384054079021,4.11156881297163 --trim3 4 --local -M 4 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s --- Summary --- 899s Read 1 reference strings 899s Checked 0 alignments, 0 edits 899s --------------- 899s PASSED 899s ALSO checking that bowtie2 and bowtie2-align match up 899s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 899s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 899s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 899s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 899s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 899s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 899s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 899s 54 reads; of these: 899s 50 (92.59%) were paired; of these: 899s 50 (100.00%) aligned concordantly 0 times 899s 0 (0.00%) aligned concordantly exactly 1 time 899s 0 (0.00%) aligned concordantly >1 times 899s ---- 899s 50 pairs aligned concordantly 0 times; of these: 899s 0 (0.00%) aligned discordantly 1 time 899s ---- 899s 50 pairs aligned 0 times concordantly or discordantly; of these: 899s 100 mates make up the pairs; of these: 899s 100 (100.00%) aligned 0 times 899s 0 (0.00%) aligned exactly 1 time 899s 0 (0.00%) aligned >1 times 899s 4 (7.41%) were unpaired; of these: 899s 4 (100.00%) aligned 0 times 899s 0 (0.00%) aligned exactly 1 time 899s 0 (0.00%) aligned >1 times 899s 0.00% overall alignment rate 899s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 899s Flattened IUPAC characters 899s Mutating sequence Sim.pm.2 899s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 899s Finished SNPs 899s Finished ref gaps 899s Finished read gaps 899s Mutating sequence Sim.pm.1 899s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 899s Finished SNPs 899s Finished ref gaps 899s Finished read gaps 899s Mutated reference genome to subject genome 899s SNPs introduced: 12 899s Reference gaps introduced: 0 899s Read gaps introduced: 0 899s Rearrangements introduced: 0 899s Created read sampler 899s Sampling 216 reads 899s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 899s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 899s parsing sequence Sim.pm.1... 899s parsing sequence Sim.pm.2... 899s Parsed 74 reference bases 899s *** Run 36 of 100 899s /usr/bin/bowtie2 --cp-ival 1 -R 2 --cp-min 4 --np 7 -M 2 --score-min L,9.70758647105882,9.20697251082988 --trim3 5 --rdg 31.410204925047 --local -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw 899s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 899s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '1' because it was < 2 characters long 899s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '3' because it was < 2 characters long 899s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '29' because it was < 2 characters long 899s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '33' because it was < 2 characters long 899s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '47' because it was < 2 characters long 899s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '50' because it was < 2 characters long 899s Warning: skipping mate #2 of read '50' because it was < 2 characters long 899s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '64' because it was < 2 characters long 899s Read 50 alignments... 899s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '68' because it was < 2 characters long 899s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '70' because it was < 2 characters long 899s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '84' because it was < 2 characters long 899s Read 100 alignments... 899s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #2 of read '86' because it was < 2 characters long 899s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 899s Warning: skipping read '97' because it was < 2 characters long 899s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '108' because it was < 2 characters long 899s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '122' because it was < 2 characters long 899s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '126' because it was < 2 characters long 899s Read 150 alignments... 899s Read 200 alignments... 899s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '135' because it was < 2 characters long 899s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '138' because it was < 2 characters long 899s Warning: skipping mate #2 of read '139' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #2 of read '139' because it was < 2 characters long 899s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '140' because it was < 2 characters long 899s Warning: skipping mate #1 of read '141' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '141' because it was < 2 characters long 899s Warning: skipping mate #2 of read '146' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #2 of read '146' because it was < 2 characters long 899s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '150' because it was < 2 characters long 899s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '151' because it was < 2 characters long 899s Warning: skipping mate #2 of read '155' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #2 of read '155' because it was < 2 characters long 899s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '156' because it was < 2 characters long 899s Warning: skipping mate #1 of read '157' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '157' because it was < 2 characters long 899s Warning: skipping mate #2 of read '170' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #2 of read '170' because it was < 2 characters long 899s Warning: skipping mate #2 of read '171' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #2 of read '171' because it was < 2 characters long 899s Warning: skipping mate #1 of read '188' because length (0) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '188' because it was < 2 characters long 899s Warning: skipping read '203' because length (0) <= # seed mismatches (0) 899s Warning: skipping read '203' because it was < 2 characters long 899s Warning: skipping mate #1 of read '213' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '213' because it was < 2 characters long 899s Warning: skipping mate #1 of read '214' because length (1) <= # seed mismatches (0) 899s Warning: skipping mate #1 of read '214' because it was < 2 characters long 899s Read 250 alignments... 899s Read 300 alignments... 899s 216 reads; of these: 899s 202 (93.52%) were paired; of these: 899s 202 (100.00%) aligned concordantly 0 times 899s 0 (0.00%) aligned concordantly exactly 1 time 899s 0 (0.00%) aligned concordantly >1 times 899s ---- 899s 202 pairs aligned concordantly 0 times; of these: 899s 0 (0.00%) aligned discordantly 1 time 899s ---- 899s 202 pairs aligned 0 times concordantly or discordantly; of these: 899s 404 mates make up the pairs; of these: 899s 404 (100.00%) aligned 0 times 899s 0 (0.00%) aligned exactly 1 time 899s 0 (0.00%) aligned >1 times 899s 14 (6.48%) were unpaired; of these: 899s 14 (100.00%) aligned 0 times 899s 0 (0.00%) aligned exactly 1 time 899s 0 (0.00%) aligned >1 times 899s 0.00% overall alignment rate 899s Read 350 alignments... 899s Read 400 alignments... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s 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line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s Processing line... 899s --- Summary --- 899s Read 1 reference strings 899s Checked 0 alignments, 0 edits 899s --------------- 899s PASSED 899s Flattened IUPAC characters 899s Mutating sequence Sim.pm.2 899s Introducing 7 SNPs, 0/2 ref/read gaps, and 0 rearrangements 899s Finished SNPs 899s Finished ref gaps 899s Finished read gaps 899s Mutating sequence Sim.pm.1 899s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 899s Finished SNPs 899s Finished ref gaps 899s Finished read gaps 899s Mutated reference genome to subject genome 899s SNPs introduced: 12 899s Reference gaps introduced: 0 899s Read gaps introduced: 2 899s Rearrangements introduced: 1 899s Created read sampler 899s Sampling 77 reads 899s *** Run 37 of 100 899s /usr/bin/bowtie2 --rdg 40.1372537955952 --mp 7.39030286025989,1.00025991444573 --cp-ival 1 --cp-min 4 --score-min L,9.59086545148099,6.72370765987558 -i C,3.6624005186856 --rfg 17.8350012418698 --trim5 4 -D 12 -R 2 -N 1 -L18 --norc -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 899s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 899s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 899s parsing sequence Sim.pm.1... 899s parsing sequence Sim.pm.2... 899s Parsed 74 reference bases 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 899s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (1) 899s Warning: skipping mate #1 of read '5' because it was < 2 characters long 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 899s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 899s Warning: skipping mate #1 of read '6' because it was < 2 characters long 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 899s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (1) 899s Warning: skipping mate #1 of read '23' because it was < 2 characters long 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 899s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 899s Warning: skipping mate #1 of read '26' because it was < 2 characters long 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 899s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (1) 899s Warning: skipping mate #2 of read '41' because it was < 2 characters long 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 899s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (1) 899s Warning: skipping mate #2 of read '46' because it was < 2 characters long 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 899s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (1) 899s Warning: skipping mate #1 of read '55' because it was < 2 characters long 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 899s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 899s Warning: skipping read '58' because it was < 2 characters long 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 899s Read 50 alignments... 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 899s Read 100 alignments... 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 899s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 899s 77 reads; of these: 900s 74 (96.10%) were paired; of these: 900s 74 (100.00%) aligned concordantly 0 times 900s 0 (0.00%) aligned concordantly exactly 1 time 900s 0 (0.00%) aligned concordantly >1 times 900s ---- 900s 74 pairs aligned concordantly 0 times; of these: 900s 0 (0.00%) aligned discordantly 1 time 900s ---- 900s 74 pairs aligned 0 times concordantly or discordantly; of these: 900s 148 mates make up the pairs; of these: 900s 138 (93.24%) aligned 0 times 900s 7 (4.73%) aligned exactly 1 time 900s 3 (2.03%) aligned >1 times 900s 3 (3.90%) were unpaired; of these: 900s 2 (66.67%) aligned 0 times 900s 0 (0.00%) aligned exactly 1 time 900s 1 (33.33%) aligned >1 times 900s 7.28% overall alignment rate 900s Read 150 alignments... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s AAAGAGGCGGGGTAACAT 900s AAAGAGGCGGGGTAACAT 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s AGAG 900s AGAG 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s AAAG 900s AAAG 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s TT 900s TT 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s TG 900s TG 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s AGGCGGGGTAACATTC 900s AGGCGGGGTAACATTC 900s Processing line... 900s Processing line... 900s GTAA 900s GTAA 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s CGGG 900s CGGG 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s TG 900s TG 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s AGGCGGGGTAACATTCAGCT 900s AGGCGGGGTAACATTCAGCT 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s CG 900s CG 900s Processing line... 900s --- Summary --- 900s Read 1 reference strings 900s Checked 11 alignments, 0 edits 900s --------------- 900s PASSED 900s Flattened IUPAC characters 900s Mutating sequence Sim.pm.2 900s Introducing 2 SNPs, 2/0 ref/read gaps, and 0 rearrangements 900s Finished SNPs 900s Finished ref gaps 900s Finished read gaps 900s Mutating sequence Sim.pm.1 900s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 900s Finished SNPs 900s Finished ref gaps 900s Finished read gaps 900s Mutated reference genome to subject genome 900s SNPs introduced: 3 900s Reference gaps introduced: 2 900s Read gaps introduced: 0 900s Rearrangements introduced: 1 900s Created read sampler 900s *** Run 38 of 100 900s /usr/bin/bowtie2 --cp-min 5 --cp-ival 1 --mm --trim3 5 --mp 8.99223686025484,5.94155161689589 --rdg 10.6605684208443,10.8780751524663 -M 2 --ma 1.55864808498187 --np 2 --norc --n-ceil 0.585479514331445,0.431344932487383 --score-min L,8.31078112331051,6.36088591100429 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 900s Sampling 96 reads 900s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 900s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 900s parsing sequence Sim.pm.1... 900s parsing sequence Sim.pm.2... 900s Parsed 74 reference bases 900s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 900s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 900s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '4' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 900s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 900s Warning: skipping mate #2 of read '10' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 900s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 900s Warning: skipping read '13' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 900s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 900s Warning: skipping mate #2 of read '21' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 900s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '25' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 900s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '27' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 900s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '39' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 900s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '52' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 900s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '58' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 900s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 900s Warning: skipping mate #2 of read '60' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 900s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '63' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 900s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '70' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 900s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '76' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 900s Read 50 alignments... 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 900s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '87' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 900s Read 100 alignments... 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 900s Warning: skipping mate #1 of read '88' because length (1) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '88' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 900s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '96' because it was < 2 characters long 900s 96 reads; of these: 900s 82 (85.42%) were paired; of these: 900s 82 (100.00%) aligned concordantly 0 times 900s 0 (0.00%) aligned concordantly exactly 1 time 900s 0 (0.00%) aligned concordantly >1 times 900s ---- 900s 82 pairs aligned concordantly 0 times; of these: 900s 0 (0.00%) aligned discordantly 1 time 900s ---- 900s 82 pairs aligned 0 times concordantly or discordantly; of these: 900s 164 mates make up the pairs; of these: 900s 153 (93.29%) aligned 0 times 900s 8 (4.88%) aligned exactly 1 time 900s 3 (1.83%) aligned >1 times 900s 14 (14.58%) were unpaired; of these: 900s 13 (92.86%) aligned 0 times 900s 0 (0.00%) aligned exactly 1 time 900s 1 (7.14%) aligned >1 times 900s 6.74% overall alignment rate 900s Read 150 alignments... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s TGT 900s TGT 900s Processing line... 900s Processing line... 900s CGGG 900s CGGG 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s TACATGA 900s TACATGA 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s CG 900s CG 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s CATG 900s CATG 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s TACA 900s TACA 900s Processing line... 900s Processing line... 900s Processing line... 900s TC 900s TC 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s GA 900s GA 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s TCAG 900s TCAG 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s CATG 900s CATG 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s CGAT 900s CGAT 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s GCGGGGTAACATTCAGCTA 900s GCGGGGTAACATTCAGCTA 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s --- Summary --- 900s Read 1 reference strings 900s Checked 12 alignments, 0 edits 900s --------------- 900s PASSED 900s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 900s /usr/bin/bowtie2 --cp-min 5 --cp-ival 1 --mm --trim3 5 --mp 8.99223686025484,5.94155161689589 --rdg 10.6605684208443,10.8780751524663 -M 2 --ma 1.55864808498187 --np 2 --norc --n-ceil 0.585479514331445,0.431344932487383 --score-min L,8.31078112331051,6.36088591100429 -q -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 900s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 900s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 900s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '4' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 900s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 900s Warning: skipping mate #2 of read '10' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 900s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 900s Warning: skipping mate #2 of read '21' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 900s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '25' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 900s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 900s Warning: skipping read '13' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 900s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '27' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 900s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '70' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 900s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '76' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 900s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '39' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 900s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '52' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 900s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '58' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 900s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 900s Warning: skipping mate #2 of read '60' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 900s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '63' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 900s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '87' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 900s Warning: skipping mate #1 of read '88' because length (1) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '88' because it was < 2 characters long 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 900s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 900s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 900s Warning: skipping mate #1 of read '96' because it was < 2 characters long 900s 96 reads; of these: 900s 82 (85.42%) were paired; of these: 900s 82 (100.00%) aligned concordantly 0 times 900s 0 (0.00%) aligned concordantly exactly 1 time 900s 0 (0.00%) aligned concordantly >1 times 900s ---- 900s 82 pairs aligned concordantly 0 times; of these: 900s 0 (0.00%) aligned discordantly 1 time 900s ---- 900s 82 pairs aligned 0 times concordantly or discordantly; of these: 900s 164 mates make up the pairs; of these: 900s 153 (93.29%) aligned 0 times 900s 8 (4.88%) aligned exactly 1 time 900s 3 (1.83%) aligned >1 times 900s 14 (14.58%) were unpaired; of these: 900s 13 (92.86%) aligned 0 times 900s 0 (0.00%) aligned exactly 1 time 900s 1 (7.14%) aligned >1 times 900s 6.74% overall alignment rate 900s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 900s Flattened IUPAC characters 900s Mutating sequence Sim.pm.1 900s Introducing 2 SNPs, 1/1 ref/read gaps, and 0 rearrangements 900s Finished SNPs 900s Finished ref gaps 900s Finished read gaps 900s Mutating sequence Sim.pm.2 900s Introducing 2 SNPs, 1/2 ref/read gaps, and 1 rearrangements 900s Finished SNPs 900s Finished ref gaps 900s Finished read gaps 900s Mutated reference genome to subject genome 900s SNPs introduced: 4 900s Reference gaps introduced: 2 900s Read gaps introduced: 3 900s Rearrangements introduced: 1 900s Created read sampler 900s Sampling 94 reads 900s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 900s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 900s parsing sequence Sim.pm.1... 900s parsing sequence Sim.pm.2... 900s Parsed 74 reference bases 900s *** Run 39 of 100 900s /usr/bin/bowtie2 --cp-ival 1 -D 47 -R 2 --cp-min 3 --nofw --score-min L,4.73563959101651,9.84898477427834 --mp 6.59465649982253,4.45439978904276 --trim5 4 --local --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq 900s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 900s 94 reads; of these: 900s 94 (100.00%) were unpaired; of these: 900s 94 (100.00%) aligned 0 times 900s 0 (0.00%) aligned exactly 1 time 900s 0 (0.00%) aligned >1 times 900s 0.00% overall alignment rate 900s Read 50 alignments... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s /usr/bin/bowtie2 --cp-ival 1 -D 47 -R 2 --cp-min 3 --nofw --score-min L,4.73563959101651,9.84898477427834 --mp 6.59465649982253,4.45439978904276 --trim5 4 --local --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s Processing line... 900s --- Summary --- 900s Read 1 reference strings 900s Checked 0 alignments, 0 edits 900s --------------- 900s PASSED 900s ALSO checking that bowtie2 and bowtie2-align match up 900s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 900s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 900s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 901s 94 reads; of these: 901s 94 (100.00%) were unpaired; of these: 901s 94 (100.00%) aligned 0 times 901s 0 (0.00%) aligned exactly 1 time 901s 0 (0.00%) aligned >1 times 901s 0.00% overall alignment rate 901s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 901s Flattened IUPAC characters 901s Mutating sequence Sim.pm.2 901s Introducing 7 SNPs, 0/1 ref/read gaps, and 1 rearrangements 901s Finished SNPs 901s Finished ref gaps 901s Finished read gaps 901s Mutating sequence Sim.pm.1 901s Introducing 4 SNPs, 0/1 ref/read gaps, and 2 rearrangements 901s Finished SNPs 901s Finished ref gaps 901s Finished read gaps 901s Mutated reference genome to subject genome 901s SNPs introduced: 11 901s Reference gaps introduced: 0 901s Read gaps introduced: 2 901s Rearrangements introduced: 3 901s Created read sampler 901s Sampling 67 reads 901s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 901s *** Run 40 of 100 901s /usr/bin/bowtie2 --cp-min 4 --mm --cp-ival 1 --mp 6.05889240280066,1.00140378862588 --local --norc -N 1 -R 1 --rfg 15.4311000223474,16.8305633215224 --score-min L,5.80524823695705,8.5322314161992 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 901s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 901s parsing sequence Sim.pm.1... 901s parsing sequence Sim.pm.2... 901s Parsed 74 reference bases 901s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #2 of read '13' because it was < 2 characters long 901s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #1 of read '17' because it was < 2 characters long 901s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #1 of read '39' because it was < 2 characters long 901s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #2 of read '40' because it was < 2 characters long 901s Warning: skipping mate #1 of read '60' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #1 of read '60' because it was < 2 characters long 901s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #2 of read '62' because it was < 2 characters long 901s Read 50 alignments... 901s 67 reads; of these: 901s 67 (100.00%) were paired; of these: 901s 67 (100.00%) aligned concordantly 0 times 901s 0 (0.00%) aligned concordantly exactly 1 time 901s 0 (0.00%) aligned concordantly >1 times 901s ---- 901s 67 pairs aligned concordantly 0 times; of these: 901s 0 (0.00%) aligned discordantly 1 time 901s ---- 901s 67 pairs aligned 0 times concordantly or discordantly; of these: 901s 134 mates make up the pairs; of these: 901s 134 (100.00%) aligned 0 times 901s 0 (0.00%) aligned exactly 1 time 901s 0 (0.00%) aligned >1 times 901s 0.00% overall alignment rate 901s Read 100 alignments... 901s Processing line... 901s Processing line... 901s /usr/bin/bowtie2 --cp-min 4 --mm --cp-ival 1 --mp 6.05889240280066,1.00140378862588 --local --norc -N 1 -R 1 --rfg 15.4311000223474,16.8305633215224 --score-min L,5.80524823695705,8.5322314161992 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s --- Summary --- 901s Read 1 reference strings 901s Checked 0 alignments, 0 edits 901s --------------- 901s PASSED 901s ALSO checking that bowtie2 and bowtie2-align match up 901s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #2 of read '13' because it was < 2 characters long 901s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #1 of read '17' because it was < 2 characters long 901s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #1 of read '39' because it was < 2 characters long 901s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #2 of read '40' because it was < 2 characters long 901s Warning: skipping mate #1 of read '60' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #1 of read '60' because it was < 2 characters long 901s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (1) 901s Warning: skipping mate #2 of read '62' because it was < 2 characters long 901s 67 reads; of these: 901s 67 (100.00%) were paired; of these: 901s 67 (100.00%) aligned concordantly 0 times 901s 0 (0.00%) aligned concordantly exactly 1 time 901s 0 (0.00%) aligned concordantly >1 times 901s ---- 901s 67 pairs aligned concordantly 0 times; of these: 901s 0 (0.00%) aligned discordantly 1 time 901s ---- 901s 67 pairs aligned 0 times concordantly or discordantly; of these: 901s 134 mates make up the pairs; of these: 901s 134 (100.00%) aligned 0 times 901s 0 (0.00%) aligned exactly 1 time 901s 0 (0.00%) aligned >1 times 901s 0.00% overall alignment rate 901s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 901s Flattened IUPAC characters 901s Mutating sequence Sim.pm.1 901s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 901s Finished SNPs 901s Finished ref gaps 901s Finished read gaps 901s Mutating sequence Sim.pm.2 901s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 901s Finished SNPs 901s Finished ref gaps 901s Finished read gaps 901s Mutated reference genome to subject genome 901s SNPs introduced: 8 901s Reference gaps introduced: 0 901s Read gaps introduced: 1 901s Rearrangements introduced: 2 901s Created read sampler 901s Sampling 50 reads 901s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 901s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 901s parsing sequence Sim.pm.1... 901s parsing sequence Sim.pm.2... 901s Parsed 74 reference bases 901s *** Run 41 of 100 901s /usr/bin/bowtie2 --local --rdg 46.4242537729729,6.17342878493548 --trim5 1 --score-min L,6.29711369017822,2.2014104407839 -M 2 --norc --np 2 --cp-min 2 --mm --cp-ival 2 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 901s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 901s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 901s Warning: skipping read '17' because it was < 2 characters long 901s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 901s Warning: skipping read '42' because it was < 2 characters long 901s 50 reads; of these: 901s 50 (100.00%) were unpaired; of these: 901s 50 (100.00%) aligned 0 times 901s 0 (0.00%) aligned exactly 1 time 901s 0 (0.00%) aligned >1 times 901s 0.00% overall alignment rate 901s Read 50 alignments... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s Processing line... 901s --- Summary --- 901s Read 1 reference strings 901s Checked 0 alignments, 0 edits 901s --------------- 901s PASSED 901s ALSO checking that bowtie2 and bowtie2-align match up 901s /usr/bin/bowtie2 --local --rdg 46.4242537729729,6.17342878493548 --trim5 1 --score-min L,6.29711369017822,2.2014104407839 -M 2 --norc --np 2 --cp-min 2 --mm --cp-ival 2 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 901s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 901s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 901s Warning: skipping read '17' because it was < 2 characters long 901s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 901s Warning: skipping read '42' because it was < 2 characters long 901s 50 reads; of these: 901s 50 (100.00%) were unpaired; of these: 901s 50 (100.00%) aligned 0 times 901s 0 (0.00%) aligned exactly 1 time 901s 0 (0.00%) aligned >1 times 901s 0.00% overall alignment rate 901s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 901s Flattened IUPAC characters 901s Mutating sequence Sim.pm.2 901s Introducing 5 SNPs, 1/0 ref/read gaps, and 2 rearrangements 901s Finished SNPs 901s Finished ref gaps 901s Finished read gaps 901s Mutating sequence Sim.pm.1 901s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 901s Finished SNPs 901s Finished ref gaps 901s Finished read gaps 901s Mutated reference genome to subject genome 901s SNPs introduced: 7 901s Reference gaps introduced: 1 901s Read gaps introduced: 1 901s Rearrangements introduced: 2 901s Created read sampler 901s Sampling 147 reads 901s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 901s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 901s parsing sequence Sim.pm.1... 901s parsing sequence Sim.pm.2... 901s Parsed 74 reference bases 901s *** Run 42 of 100 901s /usr/bin/bowtie2 --cp-min 2 --norc --cp-ival 1 --mp 4.35188330472916,3.75822055127879 --trim3 4 --trim5 7 --local --rfg 22.1421029945271,7.55422010277804 --score-min L,3.67248736189745,3.90966203032121 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq 902s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #2 of read 'R_1_1_1_59_59_1/1' because length (1) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 902s Warning: skipping mate #2 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (1) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 902s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 902s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 902s Read 50 alignments... 902s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 902s Read 100 alignments... 902s Read 150 alignments... 902s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 902s Read 200 alignments... 902s 147 reads; of these: 902s 112 (76.19%) were paired; of these: 902s 112 (100.00%) aligned concordantly 0 times 902s 0 (0.00%) aligned concordantly exactly 1 time 902s 0 (0.00%) aligned concordantly >1 times 902s ---- 902s 112 pairs aligned concordantly 0 times; of these: 902s 0 (0.00%) aligned discordantly 1 time 902s ---- 902s 112 pairs aligned 0 times concordantly or discordantly; of these: 902s 224 mates make up the pairs; of these: 902s 224 (100.00%) aligned 0 times 902s 0 (0.00%) aligned exactly 1 time 902s 0 (0.00%) aligned >1 times 902s 35 (23.81%) were unpaired; of these: 902s 35 (100.00%) aligned 0 times 902s 0 (0.00%) aligned exactly 1 time 902s 0 (0.00%) aligned >1 times 902s 0.00% overall alignment rate 902s Read 250 alignments... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s /usr/bin/bowtie2 --cp-min 2 --norc --cp-ival 1 --mp 4.35188330472916,3.75822055127879 --trim3 4 --trim5 7 --local --rfg 22.1421029945271,7.55422010277804 --score-min L,3.67248736189745,3.90966203032121 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s Processing line... 902s --- Summary --- 902s Read 1 reference strings 902s Checked 0 alignments, 0 edits 902s --------------- 902s PASSED 902s ALSO checking that bowtie2 and bowtie2-align match up 902s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #2 of read 'R_1_1_1_59_59_1/1' because length (1) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 902s Warning: skipping mate #2 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (1) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 902s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 902s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 902s 147 reads; of these: 902s 112 (76.19%) were paired; of these: 902s 112 (100.00%) aligned concordantly 0 times 902s 0 (0.00%) aligned concordantly exactly 1 time 902s 0 (0.00%) aligned concordantly >1 times 902s ---- 902s 112 pairs aligned concordantly 0 times; of these: 902s 0 (0.00%) aligned discordantly 1 time 902s ---- 902s 112 pairs aligned 0 times concordantly or discordantly; of these: 902s 224 mates make up the pairs; of these: 902s 224 (100.00%) aligned 0 times 902s 0 (0.00%) aligned exactly 1 time 902s 0 (0.00%) aligned >1 times 902s 35 (23.81%) were unpaired; of these: 902s 35 (100.00%) aligned 0 times 902s 0 (0.00%) aligned exactly 1 time 902s 0 (0.00%) aligned >1 times 902s 0.00% overall alignment rate 902s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 902s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 902s /usr/bin/bowtie2 --cp-min 2 --norc --cp-ival 1 --mp 4.35188330472916,3.75822055127879 --trim3 4 --trim5 7 --local --rfg 22.1421029945271,7.55422010277804 --score-min L,3.67248736189745,3.90966203032121 --qseq -p 3 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 902s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #2 of read 'R_1_1_1_59_59_1/1' because length (1) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 902s Warning: skipping mate #2 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (1) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 902s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 902s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 902s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 902s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 902s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 902s 147 reads; of these: 902s 112 (76.19%) were paired; of these: 902s 112 (100.00%) aligned concordantly 0 times 902s 0 (0.00%) aligned concordantly exactly 1 time 902s 0 (0.00%) aligned concordantly >1 times 902s ---- 902s 112 pairs aligned concordantly 0 times; of these: 902s 0 (0.00%) aligned discordantly 1 time 902s ---- 902s 112 pairs aligned 0 times concordantly or discordantly; of these: 902s 224 mates make up the pairs; of these: 902s 224 (100.00%) aligned 0 times 902s 0 (0.00%) aligned exactly 1 time 902s 0 (0.00%) aligned >1 times 902s 35 (23.81%) were unpaired; of these: 902s 35 (100.00%) aligned 0 times 902s 0 (0.00%) aligned exactly 1 time 902s 0 (0.00%) aligned >1 times 902s 0.00% overall alignment rate 902s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 902s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 902s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 902s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 902s /usr/bin/bowtie2 --cp-min 2 --norc --cp-ival 1 --mp 4.35188330472916,3.75822055127879 --trim3 4 --trim5 7 --local --rfg 22.1421029945271,7.55422010277804 --score-min L,3.67248736189745,3.90966203032121 --qseq -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 903s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #2 of read 'R_1_1_1_59_59_1/1' because length (1) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 903s Warning: skipping mate #2 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (1) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 903s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 903s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 903s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 903s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 903s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 903s 147 reads; of these: 903s 112 (76.19%) were paired; of these: 903s 112 (100.00%) aligned concordantly 0 times 903s 0 (0.00%) aligned concordantly exactly 1 time 903s 0 (0.00%) aligned concordantly >1 times 903s ---- 903s 112 pairs aligned concordantly 0 times; of these: 903s 0 (0.00%) aligned discordantly 1 time 903s ---- 903s 112 pairs aligned 0 times concordantly or discordantly; of these: 903s 224 mates make up the pairs; of these: 903s 224 (100.00%) aligned 0 times 903s 0 (0.00%) aligned exactly 1 time 903s 0 (0.00%) aligned >1 times 903s 35 (23.81%) were unpaired; of these: 903s 35 (100.00%) aligned 0 times 903s 0 (0.00%) aligned exactly 1 time 903s 0 (0.00%) aligned >1 times 903s 0.00% overall alignment rate 903s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 903s Flattened IUPAC characters 903s Mutating sequence Sim.pm.1 903s Introducing 1 SNPs, 1/1 ref/read gaps, and 1 rearrangements 903s Finished SNPs 903s Finished ref gaps 903s Finished read gaps 903s Mutating sequence Sim.pm.2 903s Introducing 6 SNPs, 1/2 ref/read gaps, and 1 rearrangements 903s Finished SNPs 903s Finished ref gaps 903s Finished read gaps 903s Mutated reference genome to subject genome 903s SNPs introduced: 7 903s Reference gaps introduced: 2 903s Read gaps introduced: 3 903s Rearrangements introduced: 2 903s Created read sampler 903s Sampling 34 reads 903s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 903s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 903s parsing sequence Sim.pm.1... 903s parsing sequence Sim.pm.2... 903s *** Run 43 of 100 903s /usr/bin/bowtie2 --score-min L,9.54663858910291,3.01011630979361 --rfg 5.76311464461719,18.6616177057091 -N 1 -L27 --np 5 --rdg 40.0234713423974 -a --mp 9.7139262495021,1.67806951917517 --cp-ival 1 --cp-min 4 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 903s Parsed 74 reference bases 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 903s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (1) 903s Warning: skipping mate #2 of read '25' because it was < 2 characters long 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 903s 34 reads; of these: 903s 34 (100.00%) were paired; of these: 903s 34 (100.00%) aligned concordantly 0 times 903s 0 (0.00%) aligned concordantly exactly 1 time 903s 0 (0.00%) aligned concordantly >1 times 903s ---- 903s 34 pairs aligned concordantly 0 times; of these: 903s 0 (0.00%) aligned discordantly 1 time 903s ---- 903s 34 pairs aligned 0 times concordantly or discordantly; of these: 903s 68 mates make up the pairs; of these: 903s 56 (82.35%) aligned 0 times 903s 10 (14.71%) aligned exactly 1 time 903s 2 (2.94%) aligned >1 times 903s 17.65% overall alignment rate 903s Read 50 alignments... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s GGGGTAA 903s GGGGTAA 903s Processing line... 903s Processing line... 903s AGCTA 903s AGCTA 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s GCGGGGTAA 903s GCGGGGTAA 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s ACAAAGAGGCGGGGTAACATT 903s ACAAAGAGGCGGGGTAACATT 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s TGACTCTTTACACAAAGAGGCGG 903s TGACTCTTTACACAAAGAGGCGG 903s Processing line... 903s Processing line... 903s ACACA 903s ACACA 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s TAACAT 903s TAACAT 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s AGCTA 903s AGCTA 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s ACA 903s ACA 903s Processing line... 903s ACA 903s ACA 903s Processing line... 903s ACA 903s ACA 903s Processing line... 903s ACA 903s ACA 903s Processing line... 903s ACA 903s ACA 903s Processing line... 903s TGT 903s TGT 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s AACATT 903s AACATT 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s ATGACT 903s ATGACT 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s Processing line... 903s GTG 903s GTG 903s Processing line... 903s CAC 903s CAC 903s Processing line... 903s --- Summary --- 903s Read 1 reference strings 903s Checked 18 alignments, 0 edits 903s --------------- 903s PASSED 903s ALSO checking that bowtie2 and bowtie2-align match up 903s /usr/bin/bowtie2 --score-min L,9.54663858910291,3.01011630979361 --rfg 5.76311464461719,18.6616177057091 -N 1 -L27 --np 5 --rdg 40.0234713423974 -a --mp 9.7139262495021,1.67806951917517 --cp-ival 1 --cp-min 4 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 903s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (1) 903s Warning: skipping mate #2 of read '25' because it was < 2 characters long 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 903s 34 reads; of these: 903s 34 (100.00%) were paired; of these: 903s 34 (100.00%) aligned concordantly 0 times 903s 0 (0.00%) aligned concordantly exactly 1 time 903s 0 (0.00%) aligned concordantly >1 times 903s ---- 903s 34 pairs aligned concordantly 0 times; of these: 903s 0 (0.00%) aligned discordantly 1 time 903s ---- 903s 34 pairs aligned 0 times concordantly or discordantly; of these: 903s 68 mates make up the pairs; of these: 903s 56 (82.35%) aligned 0 times 903s 10 (14.71%) aligned exactly 1 time 903s 2 (2.94%) aligned >1 times 903s 17.65% overall alignment rate 903s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 903s /usr/bin/bowtie2 --score-min L,9.54663858910291,3.01011630979361 --rfg 5.76311464461719,18.6616177057091 -N 1 -L27 --np 5 --rdg 40.0234713423974 -a --mp 9.7139262495021,1.67806951917517 --cp-ival 1 --cp-min 4 -q -p 3 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 903s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 903s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (1) 903s Warning: skipping mate #2 of read '25' because it was < 2 characters long 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 903s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 903s 34 reads; of these: 903s 34 (100.00%) were paired; of these: 903s 34 (100.00%) aligned concordantly 0 times 903s 0 (0.00%) aligned concordantly exactly 1 time 903s 0 (0.00%) aligned concordantly >1 times 903s ---- 903s 34 pairs aligned concordantly 0 times; of these: 903s 0 (0.00%) aligned discordantly 1 time 903s ---- 903s 34 pairs aligned 0 times concordantly or discordantly; of these: 903s 68 mates make up the pairs; of these: 903s 56 (82.35%) aligned 0 times 903s 10 (14.71%) aligned exactly 1 time 903s 2 (2.94%) aligned >1 times 903s 17.65% overall alignment rate 903s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 903s Flattened IUPAC characters 903s Mutating sequence Sim.pm.1 903s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 903s Finished SNPs 903s Finished ref gaps 903s Finished read gaps 903s Mutating sequence Sim.pm.2 903s Introducing 1 SNPs, 0/2 ref/read gaps, and 2 rearrangements 903s Finished SNPs 903s Finished ref gaps 903s Finished read gaps 903s Mutated reference genome to subject genome 903s SNPs introduced: 3 903s Reference gaps introduced: 0 903s Read gaps introduced: 2 903s Rearrangements introduced: 3 903s Created read sampler 903s Sampling 185 reads 903s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 903s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 903s parsing sequence Sim.pm.1... 903s parsing sequence Sim.pm.2... 903s Parsed 74 reference bases 903s *** Run 44 of 100 903s /usr/bin/bowtie2 --cp-ival 3 --cp-min 2 --trim3 0 --mp 6.37557449281394,1.59332519324154 -D 27 --nofw --score-min L,1.03378577245017,5.90811239424607 --trim5 9 --rfg 49.008701557638 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 904s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '10' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 904s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '11' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 904s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '15' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 904s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '17' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 904s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '22' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 904s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '30' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 904s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '33' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 904s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '46' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 904s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '64' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 904s Read 50 alignments... 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 904s Read 100 alignments... 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 904s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '66' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 904s Warning: skipping mate #1 of read '71' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '71' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 904s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '73' because it was < 2 characters long 904s Warning: skipping mate #2 of read '73' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 904s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '76' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 904s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '83' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 904s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '85' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 904s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '88' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 904s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '92' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 904s Warning: skipping mate #2 of read '95' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '95' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 904s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '96' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 904s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '99' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 904s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '100' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 904s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '111' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 904s Warning: skipping mate #2 of read '115' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '115' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 904s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '122' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 904s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '123' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 904s Read 150 alignments... 904s Read 200 alignments... 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 904s Warning: skipping mate #2 of read '133' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '133' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 904s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '137' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 904s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '139' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 904s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '140' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 904s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '142' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 904s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '144' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 904s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '152' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 904s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '156' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 904s Warning: skipping read '159' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '159' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 904s Warning: skipping mate #1 of read '160' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '160' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 904s Warning: skipping mate #1 of read '161' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '161' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 904s Warning: skipping mate #1 of read '165' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '165' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 904s Warning: skipping mate #1 of read '174' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '174' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 904s Warning: skipping mate #1 of read '175' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '175' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 904s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '178' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 904s Warning: skipping read '180' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '180' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 904s Warning: skipping mate #1 of read '181' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '181' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 904s Warning: skipping mate #1 of read '182' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '182' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 904s Warning: skipping mate #1 of read '184' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '184' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 904s 185 reads; of these: 904s 149 (80.54%) were paired; of these: 904s 149 (100.00%) aligned concordantly 0 times 904s 0 (0.00%) aligned concordantly exactly 1 time 904s 0 (0.00%) aligned concordantly >1 times 904s ---- 904s 149 pairs aligned concordantly 0 times; of these: 904s 3 (2.01%) aligned discordantly 1 time 904s ---- 904s 146 pairs aligned 0 times concordantly or discordantly; of these: 904s 292 mates make up the pairs; of these: 904s 259 (88.70%) aligned 0 times 904s 26 (8.90%) aligned exactly 1 time 904s 7 (2.40%) aligned >1 times 904s 36 (19.46%) were unpaired; of these: 904s 34 (94.44%) aligned 0 times 904s 2 (5.56%) aligned exactly 1 time 904s 0 (0.00%) aligned >1 times 904s 12.28% overall alignment rate 904s Read 250 alignments... 904s Read 300 alignments... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GGG 904s GGG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GAGGCGGGGTAACA 904s GAGGCGGGGTAACA 904s Processing line... 904s Processing line... 904s AGAG 904s AGAG 904s Processing line... 904s Processing line... 904s TGT 904s TGT 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GAA 904s GAA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s CGGGGTAAC 904s CGGGGTAAC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s AAA 904s AAA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GCGAT 904s GCGAT 904s Processing line... 904s Processing line... 904s ATTCAGCTACCA 904s ATTCAGCTACCA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s AG 904s AG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GAGG 904s GAGG 904s Processing line... 904s Processing line... 904s ACATGACTCTTT 904s ACATGACTCTTT 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s CGGGGTAACATTCAG 904s CGGGGTAACATTCAG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s ACTCTTTACACAAAGAGGCGG 904s ACTCTTTACACAAAGAGGCGG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TTTACACAA 904s TTTACACAA 904s Processing line... 904s CGGGGTAACA 904s CGGGGTAACA 904s Processing line... 904s Processing line... 904s Processing line... 904s TTACACAAAGAGGCGGGGTAACATTC 904s TTACACAAAGAGGCGGGGTAACATTC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TA 904s TA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TT 904s TT 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s AGC 904s AGC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TGTACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAG 904s TGTACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAG 904s Processing line... 904s AAGAGGCGGGGTAACATTCA 904s AAGAGGCGGGGTAACATTCA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s AGGCGGGGTAACATTCA 904s AGGCGGGGTAACATTCA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TG 904s TG 904s Processing line... 904s Processing line... 904s ATG 904s ATG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s ACACAAAGAGGCGGGGTA 904s ACACAAAGAGGCGGGGTA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s CTAC 904s CTAC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s CAT 904s CAT 904s Processing line... 904s Processing line... 904s GTACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAG 904s GTACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s ACACAAA 904s ACACAAA 904s Processing line... 904s GAGGC 904s GAGGC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s ATGACTCTTTACAC 904s ATGACTCTTTACAC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s ACATGACTCTTTACACAAAGAGGCGGG 904s ACATGACTCTTTACACAAAGAGGCGGG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GTACATGACTCTTTACACAAAGAGGCGGGGTAA 904s GTACATGACTCTTTACACAAAGAGGCGGGGTAA 904s Processing line... 904s TCTTTACACAAAGAGGCGGGG 904s TCTTTACACAAAGAGGCGGGG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GGCGATAAGG 904s GGCGATAAGG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s CACAAAGAGGCGGGGTAACATT 904s CACAAAGAGGCGGGGTAACATT 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TGT 904s TGT 904s Processing line... 904s Processing line... 904s Processing line... 904s CCGAACA 904s CCGAACA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GAGGCGGGGT 904s GAGGCGGGGT 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GGCGGGGT 904s GGCGGGGT 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s /usr/bin/bowtie2 --cp-ival 3 --cp-min 2 --trim3 0 --mp 6.37557449281394,1.59332519324154 -D 27 --nofw --score-min L,1.03378577245017,5.90811239424607 --trim5 9 --rfg 49.008701557638 -f -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s --- Summary --- 904s Read 1 reference strings 904s Checked 41 alignments, 0 edits 904s --------------- 904s PASSED 904s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 904s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '17' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 904s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '10' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 904s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '11' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 904s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '15' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 904s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '22' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 904s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '33' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 904s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '66' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 904s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '64' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 904s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '30' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 904s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '99' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 904s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '100' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 904s Warning: skipping mate #1 of read '71' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '71' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 904s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '83' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 904s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '85' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 904s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '88' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 904s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '92' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 904s Warning: skipping mate #2 of read '95' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '95' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 904s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '96' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 904s Warning: skipping mate #2 of read '115' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '115' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 904s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '73' because it was < 2 characters long 904s Warning: skipping mate #2 of read '73' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 904s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '46' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 904s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '76' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 904s Warning: skipping mate #2 of read '133' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '133' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 904s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '111' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 904s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '122' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 904s Warning: skipping mate #1 of read '161' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '161' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 904s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '137' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 904s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '123' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 904s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '139' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 904s Warning: skipping mate #1 of read '165' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '165' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 904s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '140' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 904s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '152' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 904s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '142' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 904s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '178' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 904s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '156' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 904s Warning: skipping read '159' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '159' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 904s Warning: skipping mate #1 of read '160' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '160' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 904s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '144' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 904s Warning: skipping read '180' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '180' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 904s Warning: skipping mate #1 of read '181' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '181' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 904s Warning: skipping mate #1 of read '182' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '182' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 904s Warning: skipping mate #1 of read '184' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '184' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 904s Warning: skipping mate #1 of read '174' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '174' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 904s Warning: skipping mate #1 of read '175' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '175' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 904s 185 reads; of these: 904s 149 (80.54%) were paired; of these: 904s 149 (100.00%) aligned concordantly 0 times 904s 0 (0.00%) aligned concordantly exactly 1 time 904s 0 (0.00%) aligned concordantly >1 times 904s ---- 904s 149 pairs aligned concordantly 0 times; of these: 904s 3 (2.01%) aligned discordantly 1 time 904s ---- 904s 146 pairs aligned 0 times concordantly or discordantly; of these: 904s 292 mates make up the pairs; of these: 904s 259 (88.70%) aligned 0 times 904s 26 (8.90%) aligned exactly 1 time 904s 7 (2.40%) aligned >1 times 904s 36 (19.46%) were unpaired; of these: 904s 34 (94.44%) aligned 0 times 904s 2 (5.56%) aligned exactly 1 time 904s 0 (0.00%) aligned >1 times 904s 12.28% overall alignment rate 904s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 904s Flattened IUPAC characters 904s Mutating sequence Sim.pm.2 904s Introducing 0 SNPs, 0/1 ref/read gaps, and 1 rearrangements 904s Finished SNPs 904s Finished ref gaps 904s Finished read gaps 904s Mutating sequence Sim.pm.1 904s Introducing 0 SNPs, 0/2 ref/read gaps, and 0 rearrangements 904s Finished SNPs 904s Finished ref gaps 904s Finished read gaps 904s Mutated reference genome to subject genome 904s SNPs introduced: 0 904s Reference gaps introduced: 0 904s Read gaps introduced: 3 904s Rearrangements introduced: 1 904s Created read sampler 904s Sampling 83 reads 904s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 904s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 904s parsing sequence Sim.pm.1... 904s parsing sequence Sim.pm.2... 904s *** Run 45 of 100 904s /usr/bin/bowtie2 -i L --trim5 6 --rdg 31.1388108203183,9.65003024612208 --mp 3.35667421543845,2.60890813765917 --score-min L,9.07652935968013,9.28204829011769 -M 4 --ma 6.30231746504874 --np 1 --nofw --cp-min 8 --mm --cp-ival 1 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 904s Parsed 74 reference bases 904s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 904s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 904s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '2' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 904s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '11' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 904s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '17' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 904s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '30' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 904s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '32' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 904s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 904s Warning: skipping read '41' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 904s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '50' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 904s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '56' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 904s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #2 of read '57' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 904s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '60' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 904s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '61' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 904s Read 50 alignments... 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 904s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '66' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 904s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '68' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 904s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '72' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 904s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 904s Warning: skipping mate #1 of read '77' because it was < 2 characters long 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 904s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 904s 83 reads; of these: 904s 76 (91.57%) were paired; of these: 904s 75 (98.68%) aligned concordantly 0 times 904s 1 (1.32%) aligned concordantly exactly 1 time 904s 0 (0.00%) aligned concordantly >1 times 904s ---- 904s 75 pairs aligned concordantly 0 times; of these: 904s 1 (1.33%) aligned discordantly 1 time 904s ---- 904s 74 pairs aligned 0 times concordantly or discordantly; of these: 904s 148 mates make up the pairs; of these: 904s 127 (85.81%) aligned 0 times 904s 14 (9.46%) aligned exactly 1 time 904s 7 (4.73%) aligned >1 times 904s 7 (8.43%) were unpaired; of these: 904s 7 (100.00%) aligned 0 times 904s 0 (0.00%) aligned exactly 1 time 904s 0 (0.00%) aligned >1 times 904s 15.72% overall alignment rate 904s Read 100 alignments... 904s Read 150 alignments... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s CATGACTCTTTACACAAAGAGGCGGGGT 904s CATGACTCTTTACACAAAGAGGCGGGGT 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GGGTGTACATGACTCTTTACACAAA 904s GGGTGTACATGACTCTTTACACAAA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s AG 904s AG 904s Processing line... 904s AAAGAGGCGGGGTAACATTCAGCTA 904s AAAGAGGCGGGGTAACATTCAGCTA 904s Processing line... 904s Processing line... 904s Processing line... 904s TCT 904s TCT 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s CTCTTTACACAAAGAGGCG 904s CTCTTTACACAAAGAGGCG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TAC 904s TAC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s CGA 904s CGA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GGG 904s GGG 904s Processing line... 904s Processing line... 904s Processing line... 904s ACA 904s ACA 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s AGAGGC 904s AGAGGC 904s Processing line... 904s TACACAAAGAGGCGGGGTAAC 904s TACACAAAGAGGCGGGGTAAC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TCTT 904s TCTT 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s AAC 904s AAC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TTACACAAAGAGGCGGGGTAAC 904s TTACACAAAGAGGCGGGGTAAC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TCAGCTA 904s TCAGCTA 904s Processing line... 904s CATGACTCTTTACACAAAGAG 904s CATGACTCTTTACACAAAGAG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s TGAC 904s TGAC 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s CTTTACACAAAGAGGCGGG 904s CTTTACACAAAGAGGCGGG 904s Processing line... 904s Processing line... 904s AAGAGGCGGGGT 904s AAGAGGCGGGGT 904s /usr/bin/bowtie2 -i L --trim5 6 --rdg 31.1388108203183,9.65003024612208 --mp 3.35667421543845,2.60890813765917 --score-min L,9.07652935968013,9.28204829011769 -M 4 --ma 6.30231746504874 --np 1 --nofw --cp-min 8 --mm --cp-ival 1 -f -p 3 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s AAGAGGCGGGGTAACATTCAG 904s AAGAGGCGGGGTAACATTCAG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s AAAGAGGCGGGGT 904s AAAGAGGCGGGGT 904s Processing line... 904s Processing line... 904s TT 904s TT 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s GTG 904s GTG 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s Processing line... 904s AAGAGGC 904s AAGAGGC 904s Processing line... 904s --- Summary --- 904s Read 1 reference strings 904s Checked 25 alignments, 0 edits 904s --------------- 904s PASSED 904s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 905s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 905s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 905s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '2' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 905s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '11' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 905s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 905s Warning: skipping read '41' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 905s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '17' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 905s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 905s Warning: skipping mate #2 of read '50' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 905s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '56' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 905s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 905s Warning: skipping mate #2 of read '57' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 905s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '66' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 905s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '68' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 905s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 905s Warning: skipping mate #2 of read '30' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 905s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '32' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 905s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '60' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 905s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '61' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 905s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '72' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 905s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '77' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 905s 83 reads; of these: 905s 76 (91.57%) were paired; of these: 905s 75 (98.68%) aligned concordantly 0 times 905s 1 (1.32%) aligned concordantly exactly 1 time 905s 0 (0.00%) aligned concordantly >1 times 905s ---- 905s 75 pairs aligned concordantly 0 times; of these: 905s 1 (1.33%) aligned discordantly 1 time 905s ---- 905s 74 pairs aligned 0 times concordantly or discordantly; of these: 905s 148 mates make up the pairs; of these: 905s 127 (85.81%) aligned 0 times 905s 14 (9.46%) aligned exactly 1 time 905s 7 (4.73%) aligned >1 times 905s 7 (8.43%) were unpaired; of these: 905s 7 (100.00%) aligned 0 times 905s 0 (0.00%) aligned exactly 1 time 905s 0 (0.00%) aligned >1 times 905s 15.72% overall alignment rate 905s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 905s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 905s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 905s Flattened IUPAC characters 905s Mutating sequence Sim.pm.2 905s Introducing 14 SNPs, 0/0 ref/read gaps, and 0 rearrangements 905s Finished SNPs 905s Finished ref gaps 905s Finished read gaps 905s Mutating sequence Sim.pm.1 905s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 905s Finished SNPs 905s Finished ref gaps 905s Finished read gaps 905s Mutated reference genome to subject genome 905s SNPs introduced: 16 905s Reference gaps introduced: 0 905s Read gaps introduced: 0 905s Rearrangements introduced: 1 905s Created read sampler 905s Sampling 38 reads 905s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 905s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 905s *** Run 46 of 100 905s /usr/bin/bowtie2 --rfg 4.48500513063066 -i C,4.67428248250578 --trim5 6 --score-min L,5.34263125160879,4.6082357935142 --n-ceil 1.06747196811955,0.645460888680153 --nofw --cp-min 3 --mm --cp-ival 1 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 905s parsing sequence Sim.pm.1... 905s parsing sequence Sim.pm.2... 905s Parsed 74 reference bases 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 905s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '5' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 905s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 905s Warning: skipping read '12' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 905s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 905s Warning: skipping mate #2 of read '19' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 905s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '32' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 905s 38 reads; of these: 905s 33 (86.84%) were paired; of these: 905s 32 (96.97%) aligned concordantly 0 times 905s 0 (0.00%) aligned concordantly exactly 1 time 905s 1 (3.03%) aligned concordantly >1 times 905s ---- 905s 32 pairs aligned concordantly 0 times; of these: 905s 0 (0.00%) aligned discordantly 1 time 905s ---- 905s 32 pairs aligned 0 times concordantly or discordantly; of these: 905s 64 mates make up the pairs; of these: 905s 58 (90.62%) aligned 0 times 905s 5 (7.81%) aligned exactly 1 time 905s 1 (1.56%) aligned >1 times 905s 5 (13.16%) were unpaired; of these: 905s 5 (100.00%) aligned 0 times 905s 0 (0.00%) aligned exactly 1 time 905s 0 (0.00%) aligned >1 times 905s 11.27% overall alignment rate 905s Read 50 alignments... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s AAGAGGCG 905s AAGAGGCG 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s AG 905s AG 905s Processing line... 905s ATG 905s ATG 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s CC 905s CC 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s TTT 905s TTT 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s GGA 905s GGA 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s ACACAAAG 905s ACACAAAG 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s GCGG 905s GCGG 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s Processing line... 905s --- Summary --- 905s Read 1 reference strings 905s Checked 8 alignments, 0 edits 905s --------------- 905s PASSED 905s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 905s /usr/bin/bowtie2 --rfg 4.48500513063066 -i C,4.67428248250578 --trim5 6 --score-min L,5.34263125160879,4.6082357935142 --n-ceil 1.06747196811955,0.645460888680153 --nofw --cp-min 3 --mm --cp-ival 1 -q -p 3 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 905s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 905s Warning: skipping mate #2 of read '19' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 905s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '5' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 905s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 905s Warning: skipping mate #1 of read '32' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 905s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 905s Warning: skipping read '12' because it was < 2 characters long 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 905s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 905s 38 reads; of these: 905s 33 (86.84%) were paired; of these: 905s 32 (96.97%) aligned concordantly 0 times 905s 0 (0.00%) aligned concordantly exactly 1 time 905s 1 (3.03%) aligned concordantly >1 times 905s ---- 905s 32 pairs aligned concordantly 0 times; of these: 905s 0 (0.00%) aligned discordantly 1 time 905s ---- 905s 32 pairs aligned 0 times concordantly or discordantly; of these: 905s 64 mates make up the pairs; of these: 905s 58 (90.62%) aligned 0 times 905s 5 (7.81%) aligned exactly 1 time 905s 1 (1.56%) aligned >1 times 905s 5 (13.16%) were unpaired; of these: 905s 5 (100.00%) aligned 0 times 905s 0 (0.00%) aligned exactly 1 time 905s 0 (0.00%) aligned >1 times 905s 11.27% overall alignment rate 905s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 905s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 905s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 905s Flattened IUPAC characters 905s Mutating sequence Sim.pm.1 905s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 905s Finished SNPs 905s Finished ref gaps 905s Finished read gaps 905s Mutating sequence Sim.pm.2 905s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 905s Finished SNPs 905s Finished ref gaps 905s Finished read gaps 905s Mutated reference genome to subject genome 905s SNPs introduced: 4 905s Reference gaps introduced: 0 905s Read gaps introduced: 0 905s Rearrangements introduced: 0 905s Created read sampler 905s Sampling 79 reads 905s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 905s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 905s parsing sequence Sim.pm.1... 905s parsing sequence Sim.pm.2... 905s Parsed 74 reference bases 905s *** Run 47 of 100 905s /usr/bin/bowtie2 --score-min L,2.60648180290635,9.8295797456588 --n-ceil 1.25269352201323,0.372265669583614 -M 2 --local -i S,2.90469980235188 --mp 4.89622019053377,4.23614145073668 --trim5 2 --cp-ival 1 --nofw --cp-min 8 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 905s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 906s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #2 of read '39' because it was < 2 characters long 906s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #1 of read '52' because it was < 2 characters long 906s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #2 of read '54' because it was < 2 characters long 906s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 906s Warning: skipping mate #1 of read '62' because it was < 2 characters long 906s Read 50 alignments... 906s Read 100 alignments... 906s 79 reads; of these: 906s 75 (94.94%) were paired; of these: 906s 75 (100.00%) aligned concordantly 0 times 906s 0 (0.00%) aligned concordantly exactly 1 time 906s 0 (0.00%) aligned concordantly >1 times 906s ---- 906s 75 pairs aligned concordantly 0 times; of these: 906s 0 (0.00%) aligned discordantly 1 time 906s ---- 906s 75 pairs aligned 0 times concordantly or discordantly; of these: 906s 150 mates make up the pairs; of these: 906s 150 (100.00%) aligned 0 times 906s 0 (0.00%) aligned exactly 1 time 906s 0 (0.00%) aligned >1 times 906s 4 (5.06%) were unpaired; of these: 906s 4 (100.00%) aligned 0 times 906s 0 (0.00%) aligned exactly 1 time 906s 0 (0.00%) aligned >1 times 906s 0.00% overall alignment rate 906s Read 150 alignments... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s /usr/bin/bowtie2 --score-min L,2.60648180290635,9.8295797456588 --n-ceil 1.25269352201323,0.372265669583614 -M 2 --local -i S,2.90469980235188 --mp 4.89622019053377,4.23614145073668 --trim5 2 --cp-ival 1 --nofw --cp-min 8 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s Processing line... 906s --- Summary --- 906s Read 1 reference strings 906s Checked 0 alignments, 0 edits 906s --------------- 906s PASSED 906s ALSO checking that bowtie2 and bowtie2-align match up 906s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 906s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #2 of read '39' because it was < 2 characters long 906s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #1 of read '52' because it was < 2 characters long 906s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #2 of read '54' because it was < 2 characters long 906s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 906s Warning: skipping mate #1 of read '62' because it was < 2 characters long 906s 79 reads; of these: 906s 75 (94.94%) were paired; of these: 906s 75 (100.00%) aligned concordantly 0 times 906s 0 (0.00%) aligned concordantly exactly 1 time 906s 0 (0.00%) aligned concordantly >1 times 906s ---- 906s 75 pairs aligned concordantly 0 times; of these: 906s 0 (0.00%) aligned discordantly 1 time 906s ---- 906s 75 pairs aligned 0 times concordantly or discordantly; of these: 906s 150 mates make up the pairs; of these: 906s 150 (100.00%) aligned 0 times 906s 0 (0.00%) aligned exactly 1 time 906s 0 (0.00%) aligned >1 times 906s 4 (5.06%) were unpaired; of these: 906s 4 (100.00%) aligned 0 times 906s 0 (0.00%) aligned exactly 1 time 906s 0 (0.00%) aligned >1 times 906s 0.00% overall alignment rate 906s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 906s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 906s /usr/bin/bowtie2 --score-min L,2.60648180290635,9.8295797456588 --n-ceil 1.25269352201323,0.372265669583614 -M 2 --local -i S,2.90469980235188 --mp 4.89622019053377,4.23614145073668 --trim5 2 --cp-ival 1 --nofw --cp-min 8 -f -p 3 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 906s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 906s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #1 of read '52' because it was < 2 characters long 906s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #2 of read '54' because it was < 2 characters long 906s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 906s Warning: skipping mate #1 of read '62' because it was < 2 characters long 906s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #2 of read '39' because it was < 2 characters long 906s 79 reads; of these: 906s 75 (94.94%) were paired; of these: 906s 75 (100.00%) aligned concordantly 0 times 906s 0 (0.00%) aligned concordantly exactly 1 time 906s 0 (0.00%) aligned concordantly >1 times 906s ---- 906s 75 pairs aligned concordantly 0 times; of these: 906s 0 (0.00%) aligned discordantly 1 time 906s ---- 906s 75 pairs aligned 0 times concordantly or discordantly; of these: 906s 150 mates make up the pairs; of these: 906s 150 (100.00%) aligned 0 times 906s 0 (0.00%) aligned exactly 1 time 906s 0 (0.00%) aligned >1 times 906s 4 (5.06%) were unpaired; of these: 906s 4 (100.00%) aligned 0 times 906s 0 (0.00%) aligned exactly 1 time 906s 0 (0.00%) aligned >1 times 906s 0.00% overall alignment rate 906s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 906s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 906s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 906s /usr/bin/bowtie2 --score-min L,2.60648180290635,9.8295797456588 --n-ceil 1.25269352201323,0.372265669583614 -M 2 --local -i S,2.90469980235188 --mp 4.89622019053377,4.23614145073668 --trim5 2 --cp-ival 1 --nofw --cp-min 8 -f -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 906s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 906s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 906s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #2 of read '39' because it was < 2 characters long 906s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #1 of read '52' because it was < 2 characters long 906s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 906s Warning: skipping mate #2 of read '54' because it was < 2 characters long 906s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 906s Warning: skipping mate #1 of read '62' because it was < 2 characters long 906s 79 reads; of these: 906s 75 (94.94%) were paired; of these: 906s 75 (100.00%) aligned concordantly 0 times 906s 0 (0.00%) aligned concordantly exactly 1 time 906s 0 (0.00%) aligned concordantly >1 times 906s ---- 906s 75 pairs aligned concordantly 0 times; of these: 906s 0 (0.00%) aligned discordantly 1 time 906s ---- 906s 75 pairs aligned 0 times concordantly or discordantly; of these: 906s 150 mates make up the pairs; of these: 906s 150 (100.00%) aligned 0 times 906s 0 (0.00%) aligned exactly 1 time 906s 0 (0.00%) aligned >1 times 906s 4 (5.06%) were unpaired; of these: 906s 4 (100.00%) aligned 0 times 906s 0 (0.00%) aligned exactly 1 time 906s 0 (0.00%) aligned >1 times 906s 0.00% overall alignment rate 906s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 906s Flattened IUPAC characters 906s Mutating sequence Sim.pm.2 906s Introducing 14 SNPs, 2/0 ref/read gaps, and 0 rearrangements 906s Finished SNPs 906s Finished ref gaps 906s Finished read gaps 906s Mutating sequence Sim.pm.1 906s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 906s Finished SNPs 906s Finished ref gaps 906s Finished read gaps 906s Mutated reference genome to subject genome 906s SNPs introduced: 14 906s Reference gaps introduced: 2 906s Read gaps introduced: 0 906s Rearrangements introduced: 1 906s Created read sampler 906s Sampling 32 reads 906s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 906s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 906s parsing sequence Sim.pm.1... 906s *** Run 48 of 100 906s /usr/bin/bowtie2 --mp 4.23392086656917,1.21031643863623 --trim3 2 --rdg 8.17776822350468 --ma 20.6712604263132 --cp-min 8 --cp-ival 1 -i S,1.85578928782702,4.84350808416409 --rfg 12.1074997997552 --trim5 7 --score-min L,9.30200325123513,2.33994374233075 --nofw -D 17 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 906s parsing sequence Sim.pm.2... 906s Parsed 74 reference bases 907s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 907s /usr/bin/bowtie2 --mp 4.23392086656917,1.21031643863623 --trim3 2 --rdg 8.17776822350468 --ma 20.6712604263132 --cp-min 8 --cp-ival 1 -i S,1.85578928782702,4.84350808416409 --rfg 12.1074997997552 --trim5 7 --score-min L,9.30200325123513,2.33994374233075 --nofw -D 17 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 907s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 907s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '8' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 907s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '11' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 907s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '12' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 907s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '16' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 907s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '18' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 907s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '24' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 907s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '28' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 907s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '32' because it was < 2 characters long 907s 32 reads; of these: 907s 32 (100.00%) were unpaired; of these: 907s 30 (93.75%) aligned 0 times 907s 1 (3.12%) aligned exactly 1 time 907s 1 (3.12%) aligned >1 times 907s 6.25% overall alignment rate 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s AC 907s AC 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s CAG 907s CAG 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s --- Summary --- 907s Read 1 reference strings 907s Checked 2 alignments, 0 edits 907s --------------- 907s PASSED 907s ALSO checking that bowtie2 and bowtie2-align match up 907s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 907s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 907s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '8' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 907s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '11' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 907s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '12' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 907s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '16' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 907s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '18' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 907s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '24' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 907s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '28' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 907s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '32' because it was < 2 characters long 907s 32 reads; of these: 907s 32 (100.00%) were unpaired; of these: 907s 30 (93.75%) aligned 0 times 907s 1 (3.12%) aligned exactly 1 time 907s 1 (3.12%) aligned >1 times 907s 6.25% overall alignment rate 907s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 907s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 907s /usr/bin/bowtie2 --mp 4.23392086656917,1.21031643863623 --trim3 2 --rdg 8.17776822350468 --ma 20.6712604263132 --cp-min 8 --cp-ival 1 -i S,1.85578928782702,4.84350808416409 --rfg 12.1074997997552 --trim5 7 --score-min L,9.30200325123513,2.33994374233075 --nofw -D 17 -q -p 2 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 907s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 907s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 907s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '8' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 907s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '11' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 907s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '12' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 907s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '16' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 907s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '18' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 907s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '24' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 907s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '28' because it was < 2 characters long 907s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 907s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 907s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '32' because it was < 2 characters long 907s 32 reads; of these: 907s 32 (100.00%) were unpaired; of these: 907s 30 (93.75%) aligned 0 times 907s 1 (3.12%) aligned exactly 1 time 907s 1 (3.12%) aligned >1 times 907s 6.25% overall alignment rate 907s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 907s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 907s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 907s Flattened IUPAC characters 907s Mutating sequence Sim.pm.1 907s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 907s Finished SNPs 907s Finished ref gaps 907s Finished read gaps 907s Mutating sequence Sim.pm.2 907s Introducing 13 SNPs, 3/0 ref/read gaps, and 1 rearrangements 907s Finished SNPs 907s Finished ref gaps 907s Finished read gaps 907s Mutated reference genome to subject genome 907s SNPs introduced: 19 907s Reference gaps introduced: 3 907s Read gaps introduced: 0 907s Rearrangements introduced: 1 907s Created read sampler 907s Sampling 54 reads 907s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 907s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 907s parsing sequence Sim.pm.1... 907s parsing sequence Sim.pm.2... 907s Parsed 74 reference bases 907s *** Run 49 of 100 907s /usr/bin/bowtie2 --score-min L,6.86002303431833,7.10948234205414 --rfg 41.0459874616512 --local --mp 9.89503496888931,4.19395284936111 --trim3 7 --trim5 6 --cp-ival 1 --nofw --np 5 --cp-min 2 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 907s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '1' because it was < 2 characters long 907s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '4' because it was < 2 characters long 907s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '18' because it was < 2 characters long 907s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '19' because it was < 2 characters long 907s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '20' because it was < 2 characters long 907s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '26' because it was < 2 characters long 907s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '27' because it was < 2 characters long 907s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '28' because it was < 2 characters long 907s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '36' because it was < 2 characters long 907s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '41' because it was < 2 characters long 907s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '42' because it was < 2 characters long 907s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '43' because it was < 2 characters long 907s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '44' because it was < 2 characters long 907s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '45' because it was < 2 characters long 907s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '46' because it was < 2 characters long 907s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '49' because it was < 2 characters long 907s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '51' because it was < 2 characters long 907s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 907s Warning: skipping read '54' because it was < 2 characters long 907s 54 reads; of these: 907s 54 (100.00%) were unpaired; of these: 907s 54 (100.00%) aligned 0 times 907s 0 (0.00%) aligned exactly 1 time 907s 0 (0.00%) aligned >1 times 907s 0.00% overall alignment rate 907s Read 50 alignments... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s Processing line... 907s --- Summary --- 907s Read 1 reference strings 907s Checked 0 alignments, 0 edits 907s --------------- 907s PASSED 907s Flattened IUPAC characters 907s Mutating sequence Sim.pm.2 907s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 907s Finished SNPs 907s Finished ref gaps 907s Finished read gaps 907s Mutating sequence Sim.pm.1 907s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 907s Finished SNPs 907s Finished ref gaps 907s Finished read gaps 907s Mutated reference genome to subject genome 907s SNPs introduced: 9 907s Reference gaps introduced: 0 907s Read gaps introduced: 0 907s Rearrangements introduced: 1 907s Created read sampler 907s Sampling 117 reads 907s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 907s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 907s parsing sequence Sim.pm.1... 907s parsing sequence Sim.pm.2... 907s Parsed 74 reference bases 907s *** Run 50 of 100 907s /usr/bin/bowtie2 --trim3 3 --mp 8.25158978876897,4.15962460849811 --rfg 49.4104984267114,8.92076884967524 -i S,1.87927592626701 --score-min L,4.84905918835198,7.74678968381003 --cp-min 2 --cp-ival 1 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 908s 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 908s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (1) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 908s 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 908s 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 908s 117 reads; of these: 908s 117 (100.00%) were unpaired; of these: 908s 101 (86.32%) aligned 0 times 908s 10 (8.55%) aligned exactly 1 time 908s 6 (5.13%) aligned >1 times 908s 13.68% overall alignment rate 908s Read 50 alignments... 908s Read 100 alignments... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s CTTT 908s CTTT 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s CTC 908s CTC 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s GAGGCGGGGTAACA 908s GAGGCGGGGTAACA 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s TCTTTACACAAAG 908s TCTTTACACAAAG 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s GGAGGG 908s GGAGGG 908s Processing line... 908s Processing line... 908s GAGG 908s GAGG 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s CA 908s CA 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s AGAGG 908s AGAGG 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s ACAAAGAGGCGG 908s ACAAAGAGGCGG 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s TTAC 908s TTAC 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s AAGAGGC 908s AAGAGGC 908s Processing line... 908s Processing line... 908s GCG 908s GCG 908s Processing line... 908s GGGCGATAAGG 908s GGGCGATAAGG 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s CGATAAGGGCCGAACAT 908s CGATAAGGGCCGAACAT 908s Processing line... 908s Processing line... 908s GGCGGGGTA 908s GGCGGGGTA 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s GCTAC 908s GCTAC 908s Processing line... 908s Processing line... 908s Processing line... 908s --- Summary --- 908s Read 1 reference strings 908s Checked 16 alignments, 0 edits 908s --------------- 908s PASSED 908s ALSO checking that bowtie2 and bowtie2-align match up 908s /usr/bin/bowtie2 --trim3 3 --mp 8.25158978876897,4.15962460849811 --rfg 49.4104984267114,8.92076884967524 -i S,1.87927592626701 --score-min L,4.84905918835198,7.74678968381003 --cp-min 2 --cp-ival 1 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 908s 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 908s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s 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 908s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (1) <= # seed mismatches (0) 908s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 908s 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 908s 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 908s 117 reads; of these: 908s 117 (100.00%) were unpaired; of these: 908s 101 (86.32%) aligned 0 times 908s 10 (8.55%) aligned exactly 1 time 908s 6 (5.13%) aligned >1 times 908s 13.68% overall alignment rate 908s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 908s Flattened IUPAC characters 908s Mutating sequence Sim.pm.2 908s Introducing 14 SNPs, 1/2 ref/read gaps, and 0 rearrangements 908s Finished SNPs 908s Finished ref gaps 908s Finished read gaps 908s Mutating sequence Sim.pm.1 908s Introducing 8 SNPs, 2/0 ref/read gaps, and 2 rearrangements 908s Finished SNPs 908s Finished ref gaps 908s Finished read gaps 908s Mutated reference genome to subject genome 908s SNPs introduced: 22 908s Reference gaps introduced: 3 908s Read gaps introduced: 2 908s Rearrangements introduced: 2 908s Created read sampler 908s Sampling 139 reads 908s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 908s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 908s parsing sequence Sim.pm.1... 908s parsing sequence Sim.pm.2... 908s Parsed 74 reference bases 908s *** Run 51 of 100 908s /usr/bin/bowtie2 -k 6 --mp 5.14064464809131,3.6595602999733 --trim3 6 --rdg 9.68709815172634,9.98946325672063 --local --cp-ival 1 --mm --cp-min 5 --score-min L,7.12281000029242,6.19579075539588 --trim5 3 -i S,2.57157947802183 --np 2 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 908s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '14' because it was < 2 characters long 908s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '18' because it was < 2 characters long 908s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '19' because it was < 2 characters long 908s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '21' because it was < 2 characters long 908s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '25' because it was < 2 characters long 908s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '26' because it was < 2 characters long 908s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '28' because it was < 2 characters long 908s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '36' because it was < 2 characters long 908s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '37' because it was < 2 characters long 908s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '39' because it was < 2 characters long 908s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '42' because it was < 2 characters long 908s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '45' because it was < 2 characters long 908s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '49' because it was < 2 characters long 908s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '51' because it was < 2 characters long 908s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '59' because it was < 2 characters long 908s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '61' because it was < 2 characters long 908s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '67' because it was < 2 characters long 908s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '69' because it was < 2 characters long 908s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '70' because it was < 2 characters long 908s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '77' because it was < 2 characters long 908s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '87' because it was < 2 characters long 908s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '89' because it was < 2 characters long 908s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '90' because it was < 2 characters long 908s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '96' because it was < 2 characters long 908s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '106' because it was < 2 characters long 908s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '108' because it was < 2 characters long 908s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '109' because it was < 2 characters long 908s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '117' because it was < 2 characters long 908s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '126' because it was < 2 characters long 908s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '129' because it was < 2 characters long 908s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '135' because it was < 2 characters long 908s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '136' because it was < 2 characters long 908s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '137' because it was < 2 characters long 908s 139 reads; of these: 908s 139 (100.00%) were unpaired; of these: 908s 139 (100.00%) aligned 0 times 908s 0 (0.00%) aligned exactly 1 time 908s 0 (0.00%) aligned >1 times 908s 0.00% overall alignment rate 908s Read 50 alignments... 908s Read 100 alignments... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s Processing line... 908s --- Summary --- 908s Read 1 reference strings 908s Checked 0 alignments, 0 edits 908s --------------- 908s PASSED 908s ALSO checking that bowtie2 and bowtie2-align match up 908s /usr/bin/bowtie2 -k 6 --mp 5.14064464809131,3.6595602999733 --trim3 6 --rdg 9.68709815172634,9.98946325672063 --local --cp-ival 1 --mm --cp-min 5 --score-min L,7.12281000029242,6.19579075539588 --trim5 3 -i S,2.57157947802183 --np 2 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 908s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '14' because it was < 2 characters long 908s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '18' because it was < 2 characters long 908s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '19' because it was < 2 characters long 908s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '21' because it was < 2 characters long 908s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '25' because it was < 2 characters long 908s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '26' because it was < 2 characters long 908s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '28' because it was < 2 characters long 908s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '36' because it was < 2 characters long 908s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '37' because it was < 2 characters long 908s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '39' because it was < 2 characters long 908s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '42' because it was < 2 characters long 908s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '45' because it was < 2 characters long 908s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '49' because it was < 2 characters long 908s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '51' because it was < 2 characters long 908s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '59' because it was < 2 characters long 908s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '61' because it was < 2 characters long 908s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '67' because it was < 2 characters long 908s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '69' because it was < 2 characters long 908s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '70' because it was < 2 characters long 908s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '77' because it was < 2 characters long 908s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '87' because it was < 2 characters long 908s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '89' because it was < 2 characters long 908s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '90' because it was < 2 characters long 908s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '96' because it was < 2 characters long 908s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '106' because it was < 2 characters long 908s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '108' because it was < 2 characters long 908s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '109' because it was < 2 characters long 908s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '117' because it was < 2 characters long 908s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '126' because it was < 2 characters long 908s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '129' because it was < 2 characters long 908s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '135' because it was < 2 characters long 908s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '136' because it was < 2 characters long 908s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 908s Warning: skipping read '137' because it was < 2 characters long 908s 139 reads; of these: 908s 139 (100.00%) were unpaired; of these: 908s 139 (100.00%) aligned 0 times 908s 0 (0.00%) aligned exactly 1 time 908s 0 (0.00%) aligned >1 times 908s 0.00% overall alignment rate 908s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 908s Flattened IUPAC characters 908s Mutating sequence Sim.pm.2 908s Introducing 2 SNPs, 1/0 ref/read gaps, and 2 rearrangements 908s Finished SNPs 908s Finished ref gaps 908s Finished read gaps 908s Mutating sequence Sim.pm.1 908s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 908s Finished SNPs 908s Finished ref gaps 908s Finished read gaps 908s Mutated reference genome to subject genome 908s SNPs introduced: 4 908s Reference gaps introduced: 1 908s Read gaps introduced: 0 908s Rearrangements introduced: 3 908s Created read sampler 908s Sampling 60 reads 908s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 908s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 908s parsing sequence Sim.pm.1... 908s parsing sequence Sim.pm.2... 908s Parsed 74 reference bases 908s *** Run 52 of 100 908s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 -M 5 --ma 39.3936651286024 --rdg 19.5758064775465,6.34346470059571 --mp 7.94040994901902,3.4304976838605 --trim3 5 -D 41 --score-min L,1.97294561783801,3.58432339954539 --n-ceil 0.288038126418014,0.988178225697554 --trim5 3 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 909s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 909s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 909s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 909s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '6' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 909s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '13' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 909s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '17' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 909s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 909s Warning: skipping read '25' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 909s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '26' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 909s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 909s Warning: skipping mate #2 of read '27' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 909s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '38' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 909s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '40' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 909s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '47' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 909s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 909s Warning: skipping read '49' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 909s 60 reads; of these: 909s 47 (78.33%) were paired; of these: 909s 47 (100.00%) aligned concordantly 0 times 909s 0 (0.00%) aligned concordantly exactly 1 time 909s 0 (0.00%) aligned concordantly >1 times 909s ---- 909s 47 pairs aligned concordantly 0 times; of these: 909s 0 (0.00%) aligned discordantly 1 time 909s ---- 909s 47 pairs aligned 0 times concordantly or discordantly; of these: 909s 94 mates make up the pairs; of these: 909s 74 (78.72%) aligned 0 times 909s 14 (14.89%) aligned exactly 1 time 909s 6 (6.38%) aligned >1 times 909s 13 (21.67%) were unpaired; of these: 909s 8 (61.54%) aligned 0 times 909s 2 (15.38%) aligned exactly 1 time 909s 3 (23.08%) aligned >1 times 909s 23.36% overall alignment rate 909s Read 50 alignments... 909s Read 100 alignments... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s GCT 909s GCT 909s Processing line... 909s Processing line... 909s Processing line... 909s CTTTACACAAAGAGGC 909s CTTTACACAAAGAGGC 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s GGGG 909s GGGG 909s Processing line... 909s Processing line... 909s TACATGACTCTT 909s TACATGACTCTT 909s Processing line... 909s Processing line... 909s GACTCTTTA 909s GACTCTTTA 909s Processing line... 909s Processing line... 909s GACTCTTTACACAAAGAGGCGGGGTAACATTCAGC 909s GACTCTTTACACAAAGAGGCGGGGTAACATTCAGC 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s CTCT 909s CTCT 909s Processing line... 909s GACTCTTTACACAAAGAGG 909s GACTCTTTACACAAAGAGG 909s Processing line... 909s Processing line... 909s CGAT 909s CGAT 909s Processing line... 909s Processing line... 909s Processing line... 909s TACACAAA 909s TACACAAA 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s CACAAAGAGGCGGGG 909s CACAAAGAGGCGGGG 909s Processing line... 909s Processing line... 909s CTTTACACAAAGAGGCGGGGTAACAT 909s CTTTACACAAAGAGGCGGGGTAACAT 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s ACATTC 909s ACATTC 909s Processing line... 909s Processing line... 909s AGGC 909s AGGC 909s Processing line... 909s GG 909s GG 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s ATA 909s ATA 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s GTA 909s GTA 909s Processing line... 909s Processing line... 909s TCAGCTA 909s TCAGCTA 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s GGTGTACATGACTCTTTACACAAAGAGGCGGGGTAACAT 909s GGTGTACATGACTCTTTACACAAAGAGGCGGGGTAACAT 909s Processing line... 909s Processing line... 909s ACTCTTTA 909s ACTCTTTA 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s AC 909s AC 909s Processing line... 909s Processing line... 909s GGT 909s GGT 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s ACTCTTTACACAAAGAG 909s ACTCTTTACACAAAGAG 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s GA 909s GA 909s Processing line... 909s Processing line... 909s AG 909s AG 909s Processing line... 909s Processing line... 909s Processing line... 909s --- Summary --- 909s Read 1 reference strings 909s Checked 25 alignments, 0 edits 909s --------------- 909s PASSED 909s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 909s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 -M 5 --ma 39.3936651286024 --rdg 19.5758064775465,6.34346470059571 --mp 7.94040994901902,3.4304976838605 --trim3 5 -D 41 --score-min L,1.97294561783801,3.58432339954539 --n-ceil 0.288038126418014,0.988178225697554 --trim5 3 -f -p 3 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 909s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 909s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 909s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 909s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '6' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 909s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '17' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 909s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '13' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 909s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 909s Warning: skipping read '49' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 909s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 909s Warning: skipping read '25' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 909s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '26' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 909s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 909s Warning: skipping mate #2 of read '27' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 909s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '38' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 909s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '40' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 909s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '47' because it was < 2 characters long 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 909s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 909s 60 reads; of these: 909s 47 (78.33%) were paired; of these: 909s 47 (100.00%) aligned concordantly 0 times 909s 0 (0.00%) aligned concordantly exactly 1 time 909s 0 (0.00%) aligned concordantly >1 times 909s ---- 909s 47 pairs aligned concordantly 0 times; of these: 909s 0 (0.00%) aligned discordantly 1 time 909s ---- 909s 47 pairs aligned 0 times concordantly or discordantly; of these: 909s 94 mates make up the pairs; of these: 909s 74 (78.72%) aligned 0 times 909s 14 (14.89%) aligned exactly 1 time 909s 6 (6.38%) aligned >1 times 909s 13 (21.67%) were unpaired; of these: 909s 8 (61.54%) aligned 0 times 909s 2 (15.38%) aligned exactly 1 time 909s 3 (23.08%) aligned >1 times 909s 23.36% overall alignment rate 909s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 909s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 909s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 909s Flattened IUPAC characters 909s Mutating sequence Sim.pm.2 909s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 909s Finished SNPs 909s Finished ref gaps 909s Finished read gaps 909s Mutating sequence Sim.pm.1 909s Introducing 11 SNPs, 0/1 ref/read gaps, and 0 rearrangements 909s Finished SNPs 909s Finished ref gaps 909s Finished read gaps 909s Mutated reference genome to subject genome 909s SNPs introduced: 20 909s Reference gaps introduced: 0 909s Read gaps introduced: 1 909s Rearrangements introduced: 0 909s Created read sampler 909s Sampling 73 reads 909s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 909s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 909s parsing sequence Sim.pm.1... 909s parsing sequence Sim.pm.2... 909s Parsed 74 reference bases 909s *** Run 53 of 100 909s /usr/bin/bowtie2 -a --local --mm --cp-ival 4 --cp-min 5 --score-min L,5.93338547616162,5.13876785607788 --trim5 0 -i L,0.26113963252719 --rfg 27.240392571517 -R 4 --np 1 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 909s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 909s Warning: skipping mate #2 of read '5' because it was < 2 characters long 909s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '11' because it was < 2 characters long 909s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 909s Warning: skipping mate #1 of read '16' because it was < 2 characters long 909s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 909s Warning: skipping mate #2 of read '58' because it was < 2 characters long 909s Read 50 alignments... 909s 73 reads; of these: 909s 73 (100.00%) were paired; of these: 909s 73 (100.00%) aligned concordantly 0 times 909s 0 (0.00%) aligned concordantly exactly 1 time 909s 0 (0.00%) aligned concordantly >1 times 909s ---- 909s 73 pairs aligned concordantly 0 times; of these: 909s 0 (0.00%) aligned discordantly 1 time 909s ---- 909s 73 pairs aligned 0 times concordantly or discordantly; of these: 909s 146 mates make up the pairs; of these: 909s 146 (100.00%) aligned 0 times 909s 0 (0.00%) aligned exactly 1 time 909s 0 (0.00%) aligned >1 times 909s 0.00% overall alignment rate 909s Read 100 alignments... 909s Read 150 alignments... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s Processing line... 909s --- Summary --- 909s Read 1 reference strings 909s Checked 0 alignments, 0 edits 909s --------------- 909s PASSED 909s Flattened IUPAC characters 909s Mutating sequence Sim.pm.1 909s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 909s Finished SNPs 909s Finished ref gaps 909s Finished read gaps 909s Mutating sequence Sim.pm.2 909s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 909s Finished SNPs 909s Finished ref gaps 909s Finished read gaps 909s Mutated reference genome to subject genome 909s SNPs introduced: 2 909s Reference gaps introduced: 0 909s Read gaps introduced: 0 909s Rearrangements introduced: 1 909s Created read sampler 909s Sampling 63 reads 909s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 909s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 909s parsing sequence Sim.pm.1... 909s parsing sequence Sim.pm.2... 909s Parsed 74 reference bases 909s *** Run 54 of 100 909s /usr/bin/bowtie2 --local --mp 4.64425664244304,1.22175430452876 --trim3 6 -a --cp-min 10 --cp-ival 1 --mm --trim5 0 --score-min L,3.07852974146373,6.55935160375428 --np 4 -D 6 -N 1 -L25 -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 909s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 909s Warning: skipping read '5' because it was < 2 characters long 909s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 909s Warning: skipping read '8' because it was < 2 characters long 909s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 909s Warning: skipping read '21' because it was < 2 characters long 909s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 909s Warning: skipping read '22' because it was < 2 characters long 909s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 909s Warning: skipping read '25' because it was < 2 characters long 909s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 909s Warning: skipping read '29' because it was < 2 characters long 909s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 909s Warning: skipping read '41' because it was < 2 characters long 909s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 909s Warning: skipping read '43' because it was < 2 characters long 909s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 909s Warning: skipping read '48' because it was < 2 characters long 909s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 910s Warning: skipping read '55' because it was < 2 characters long 910s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 910s Warning: skipping read '61' because it was < 2 characters long 910s 63 reads; of these: 910s 63 (100.00%) were unpaired; of these: 910s 63 (100.00%) aligned 0 times 910s 0 (0.00%) aligned exactly 1 time 910s 0 (0.00%) aligned >1 times 910s 0.00% overall alignment rate 910s Read 50 alignments... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s --- Summary --- 910s Read 1 reference strings 910s Checked 0 alignments, 0 edits 910s --------------- 910s PASSED 910s Flattened IUPAC characters 910s Mutating sequence Sim.pm.2 910s Introducing 1 SNPs, 1/1 ref/read gaps, and 4 rearrangements 910s Finished SNPs 910s Finished ref gaps 910s Finished read gaps 910s Mutating sequence Sim.pm.1 910s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 910s Finished SNPs 910s Finished ref gaps 910s Finished read gaps 910s Mutated reference genome to subject genome 910s SNPs introduced: 3 910s Reference gaps introduced: 1 910s Read gaps introduced: 1 910s Rearrangements introduced: 4 910s Created read sampler 910s Sampling 144 reads 910s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 910s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 910s parsing sequence Sim.pm.1... 910s parsing sequence Sim.pm.2... 910s Parsed 74 reference bases 910s *** Run 55 of 100 910s /usr/bin/bowtie2 --cp-min 4 --cp-ival 1 --local --trim3 7 --nofw --np 1 -D 19 --trim5 9 --score-min L,6.68254521722735,3.17081960361435 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq 910s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 910s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 910s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 910s Read 50 alignments... 910s Read 100 alignments... 910s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 910s Read 150 alignments... 910s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (1) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_141_141_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 910s 144 reads; of these: 910s 101 (70.14%) were paired; of these: 910s 101 (100.00%) aligned concordantly 0 times 910s 0 (0.00%) aligned concordantly exactly 1 time 910s 0 (0.00%) aligned concordantly >1 times 910s ---- 910s 101 pairs aligned concordantly 0 times; of these: 910s 0 (0.00%) aligned discordantly 1 time 910s ---- 910s 101 pairs aligned 0 times concordantly or discordantly; of these: 910s 202 mates make up the pairs; of these: 910s 202 (100.00%) aligned 0 times 910s 0 (0.00%) aligned exactly 1 time 910s 0 (0.00%) aligned >1 times 910s 43 (29.86%) were unpaired; of these: 910s 43 (100.00%) aligned 0 times 910s 0 (0.00%) aligned exactly 1 time 910s 0 (0.00%) aligned >1 times 910s 0.00% overall alignment rate 910s Read 200 alignments... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s Processing line... 910s --- Summary --- 910s Read 1 reference strings 910s Checked 0 alignments, 0 edits 910s --------------- 910s PASSED 910s ALSO checking that bowtie2 and bowtie2-align match up 910s /usr/bin/bowtie2 --cp-min 4 --cp-ival 1 --local --trim3 7 --nofw --np 1 -D 19 --trim5 9 --score-min L,6.68254521722735,3.17081960361435 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 910s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 910s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 910s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (1) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_141_141_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 910s 144 reads; of these: 910s 101 (70.14%) were paired; of these: 910s 101 (100.00%) aligned concordantly 0 times 910s 0 (0.00%) aligned concordantly exactly 1 time 910s 0 (0.00%) aligned concordantly >1 times 910s ---- 910s 101 pairs aligned concordantly 0 times; of these: 910s 0 (0.00%) aligned discordantly 1 time 910s ---- 910s 101 pairs aligned 0 times concordantly or discordantly; of these: 910s 202 mates make up the pairs; of these: 910s 202 (100.00%) aligned 0 times 910s 0 (0.00%) aligned exactly 1 time 910s 0 (0.00%) aligned >1 times 910s 43 (29.86%) were unpaired; of these: 910s 43 (100.00%) aligned 0 times 910s 0 (0.00%) aligned exactly 1 time 910s 0 (0.00%) aligned >1 times 910s 0.00% overall alignment rate 910s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 910s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 910s /usr/bin/bowtie2 --cp-min 4 --cp-ival 1 --local --trim3 7 --nofw --np 1 -D 19 --trim5 9 --score-min L,6.68254521722735,3.17081960361435 --qseq -p 3 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 910s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 910s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 910s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (1) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 910s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 910s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 910s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 911s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 911s Warning: skipping read 'R_1_1_1_141_141_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 911s 144 reads; of these: 911s 101 (70.14%) were paired; of these: 911s 101 (100.00%) aligned concordantly 0 times 911s 0 (0.00%) aligned concordantly exactly 1 time 911s 0 (0.00%) aligned concordantly >1 times 911s ---- 911s 101 pairs aligned concordantly 0 times; of these: 911s 0 (0.00%) aligned discordantly 1 time 911s ---- 911s 101 pairs aligned 0 times concordantly or discordantly; of these: 911s 202 mates make up the pairs; of these: 911s 202 (100.00%) aligned 0 times 911s 0 (0.00%) aligned exactly 1 time 911s 0 (0.00%) aligned >1 times 911s 43 (29.86%) were unpaired; of these: 911s 43 (100.00%) aligned 0 times 911s 0 (0.00%) aligned exactly 1 time 911s 0 (0.00%) aligned >1 times 911s 0.00% overall alignment rate 911s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 911s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 911s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 911s Flattened IUPAC characters 911s Mutating sequence Sim.pm.1 911s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 911s Finished SNPs 911s Finished ref gaps 911s Finished read gaps 911s Mutating sequence Sim.pm.2 911s Introducing 4 SNPs, 2/0 ref/read gaps, and 2 rearrangements 911s Finished SNPs 911s Finished ref gaps 911s Finished read gaps 911s Mutated reference genome to subject genome 911s SNPs introduced: 7 911s Reference gaps introduced: 3 911s Read gaps introduced: 0 911s Rearrangements introduced: 2 911s Created read sampler 911s Sampling 96 reads 911s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 911s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 911s parsing sequence Sim.pm.1... 911s *** Run 56 of 100 911s /usr/bin/bowtie2 --score-min L,6.99871335406352,4.07411040053674 --gbar 2 --trim5 4 -D 21 -N 0 -L30 --np 2 --local --trim3 2 --rdg 25.9387185889255,14.9256061486325 --cp-ival 2 --cp-min 6 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq 911s parsing sequence Sim.pm.2... 911s Parsed 74 reference bases 911s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 911s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 911s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 911s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 911s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 911s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 911s Read 50 alignments... 911s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 911s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 911s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 911s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 911s 96 reads; of these: 911s 78 (81.25%) were paired; of these: 911s 78 (100.00%) aligned concordantly 0 times 911s 0 (0.00%) aligned concordantly exactly 1 time 911s 0 (0.00%) aligned concordantly >1 times 911s ---- 911s 78 pairs aligned concordantly 0 times; of these: 911s 0 (0.00%) aligned discordantly 1 time 911s ---- 911s 78 pairs aligned 0 times concordantly or discordantly; of these: 911s 156 mates make up the pairs; of these: 911s 156 (100.00%) aligned 0 times 911s 0 (0.00%) aligned exactly 1 time 911s 0 (0.00%) aligned >1 times 911s 18 (18.75%) were unpaired; of these: 911s 18 (100.00%) aligned 0 times 911s 0 (0.00%) aligned exactly 1 time 911s 0 (0.00%) aligned >1 times 911s 0.00% overall alignment rate 911s Read 100 alignments... 911s Read 150 alignments... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s --- Summary --- 911s Read 1 reference strings 911s Checked 0 alignments, 0 edits 911s --------------- 911s PASSED 911s Flattened IUPAC characters 911s Mutating sequence Sim.pm.1 911s Introducing 12 SNPs, 0/0 ref/read gaps, and 1 rearrangements 911s Finished SNPs 911s Finished ref gaps 911s Finished read gaps 911s Mutating sequence Sim.pm.2 911s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 911s Finished SNPs 911s Finished ref gaps 911s Finished read gaps 911s Mutated reference genome to subject genome 911s SNPs introduced: 16 911s Reference gaps introduced: 0 911s Read gaps introduced: 1 911s Rearrangements introduced: 1 911s Created read sampler 911s Sampling 49 reads 911s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 911s *** Run 57 of 100 911s /usr/bin/bowtie2 --score-min L,1.99854903476158,8.95604064933185 --trim5 0 -i S,1.74729195773593 --rfg 2.47643884573937,10.5492510356411 --cp-ival 1 --cp-min 15 -k 3 --rdg 36.8045354873806 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 911s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 911s parsing sequence Sim.pm.1... 911s parsing sequence Sim.pm.2... 911s Parsed 74 reference bases 911s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 911s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 911s Warning: skipping read '5' because it was < 2 characters long 911s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 911s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 911s Warning: skipping read '9' because it was < 2 characters long 911s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 911s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 911s Warning: skipping read '32' because it was < 2 characters long 911s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 911s 49 reads; of these: 911s 49 (100.00%) were unpaired; of these: 911s 43 (87.76%) aligned 0 times 911s 3 (6.12%) aligned exactly 1 time 911s 3 (6.12%) aligned >1 times 911s 12.24% overall alignment rate 911s Read 50 alignments... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s GGG 911s GGG 911s Processing line... 911s GGG 911s GGG 911s Processing line... 911s GGG 911s GGG 911s Processing line... 911s Processing line... 911s CATA 911s CATA 911s Processing line... 911s Processing line... 911s Processing line... 911s TG 911s TG 911s Processing line... 911s CA 911s CA 911s Processing line... 911s TG 911s TG 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s CGGGGT 911s CGGGGT 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s /usr/bin/bowtie2 --score-min L,1.99854903476158,8.95604064933185 --trim5 0 -i S,1.74729195773593 --rfg 2.47643884573937,10.5492510356411 --cp-ival 1 --cp-min 15 -k 3 --rdg 36.8045354873806 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s GAGGGCGATAAGGGCCG 911s GAGGGCGATAAGGGCCG 911s Processing line... 911s Processing line... 911s GTAA 911s GTAA 911s Processing line... 911s TTAC 911s TTAC 911s Processing line... 911s Processing line... 911s Processing line... 911s Processing line... 911s --- Summary --- 911s Read 1 reference strings 911s Checked 11 alignments, 0 edits 911s --------------- 911s PASSED 911s ALSO checking that bowtie2 and bowtie2-align match up 911s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 911s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 911s Warning: skipping read '5' because it was < 2 characters long 911s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 911s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 911s Warning: skipping read '9' because it was < 2 characters long 911s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 911s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 911s Warning: skipping read '32' because it was < 2 characters long 911s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 911s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 911s 49 reads; of these: 911s 49 (100.00%) were unpaired; of these: 911s 43 (87.76%) aligned 0 times 911s 3 (6.12%) aligned exactly 1 time 911s 3 (6.12%) aligned >1 times 911s 12.24% overall alignment rate 911s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 911s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 911s /usr/bin/bowtie2 --score-min L,1.99854903476158,8.95604064933185 --trim5 0 -i S,1.74729195773593 --rfg 2.47643884573937,10.5492510356411 --cp-ival 1 --cp-min 15 -k 3 --rdg 36.8045354873806 -q -p 4 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 912s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 912s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 912s Warning: skipping read '5' because it was < 2 characters long 912s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 912s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 912s Warning: skipping read '9' because it was < 2 characters long 912s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 912s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 912s Warning: skipping read '32' because it was < 2 characters long 912s 49 reads; of these: 912s 49 (100.00%) were unpaired; of these: 912s 43 (87.76%) aligned 0 times 912s 3 (6.12%) aligned exactly 1 time 912s 3 (6.12%) aligned >1 times 912s 12.24% overall alignment rate 912s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 912s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 912s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 912s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 912s /usr/bin/bowtie2 --score-min L,1.99854903476158,8.95604064933185 --trim5 0 -i S,1.74729195773593 --rfg 2.47643884573937,10.5492510356411 --cp-ival 1 --cp-min 15 -k 3 --rdg 36.8045354873806 -q -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 912s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 912s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 912s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 912s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 912s Warning: skipping read '5' because it was < 2 characters long 912s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 912s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 912s Warning: skipping read '9' because it was < 2 characters long 912s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 912s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 912s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 912s Warning: skipping read '32' because it was < 2 characters long 912s 49 reads; of these: 912s 49 (100.00%) were unpaired; of these: 912s 43 (87.76%) aligned 0 times 912s 3 (6.12%) aligned exactly 1 time 912s 3 (6.12%) aligned >1 times 912s 12.24% overall alignment rate 912s Flattened IUPAC characters 912s Mutating sequence Sim.pm.2 912s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 912s Finished SNPs 912s Finished ref gaps 912s Finished read gaps 912s Mutating sequence Sim.pm.1 912s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 912s Finished SNPs 912s Finished ref gaps 912s Finished read gaps 912s Mutated reference genome to subject genome 912s SNPs introduced: 5 912s Reference gaps introduced: 1 912s Read gaps introduced: 2 912s Rearrangements introduced: 0 912s Created read sampler 912s Sampling 99 reads 912s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 912s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 912s parsing sequence Sim.pm.1... 912s parsing sequence Sim.pm.2... 912s Parsed 74 reference bases 912s *** Run 58 of 100 912s /usr/bin/bowtie2 --cp-min 4 --cp-ival 1 --mm --local --rdg 41.5437350511632,3.91235032470421 --np 2 --norc --trim5 4 --score-min L,5.34202035333576,3.71272648339241 -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw 912s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 912s Warning: skipping mate #2 of read '5' because it was < 2 characters long 912s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 912s Warning: skipping mate #1 of read '14' because it was < 2 characters long 912s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 912s Warning: skipping mate #1 of read '25' because it was < 2 characters long 912s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 912s Warning: skipping mate #1 of read '30' because it was < 2 characters long 912s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 912s Warning: skipping mate #1 of read '40' because it was < 2 characters long 912s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 912s Warning: skipping mate #1 of read '42' because it was < 2 characters long 912s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 912s Warning: skipping mate #2 of read '57' because it was < 2 characters long 912s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 912s Read 50 alignments... 912s Warning: skipping mate #1 of read '67' because it was < 2 characters long 912s Read 100 alignments... 912s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 912s Warning: skipping read '79' because it was < 2 characters long 912s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 912s Warning: skipping mate #2 of read '85' because it was < 2 characters long 912s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 912s Warning: skipping mate #1 of read '93' because it was < 2 characters long 912s 99 reads; of these: 912s 94 (94.95%) were paired; of these: 912s 94 (100.00%) aligned concordantly 0 times 912s 0 (0.00%) aligned concordantly exactly 1 time 912s 0 (0.00%) aligned concordantly >1 times 912s ---- 912s 94 pairs aligned concordantly 0 times; of these: 912s 0 (0.00%) aligned discordantly 1 time 912s ---- 912s 94 pairs aligned 0 times concordantly or discordantly; of these: 912s 188 mates make up the pairs; of these: 912s 188 (100.00%) aligned 0 times 912s 0 (0.00%) aligned exactly 1 time 912s 0 (0.00%) aligned >1 times 912s 5 (5.05%) were unpaired; of these: 912s 5 (100.00%) aligned 0 times 912s 0 (0.00%) aligned exactly 1 time 912s 0 (0.00%) aligned >1 times 912s 0.00% overall alignment rate 912s Read 150 alignments... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s Processing line... 912s --- Summary --- 912s Read 1 reference strings 912s Checked 0 alignments, 0 edits 912s --------------- 912s PASSED 912s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 912s /usr/bin/bowtie2 --cp-min 4 --cp-ival 1 --mm --local --rdg 41.5437350511632,3.91235032470421 --np 2 --norc --trim5 4 --score-min L,5.34202035333576,3.71272648339241 -r -p 4 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 912s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 912s Warning: skipping mate #2 of read '5' because it was < 2 characters long 912s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 912s Warning: skipping mate #1 of read '14' because it was < 2 characters long 912s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '40' because it was < 2 characters long 913s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '42' because it was < 2 characters long 913s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '25' because it was < 2 characters long 913s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '30' because it was < 2 characters long 913s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '67' because it was < 2 characters long 913s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 913s Warning: skipping mate #2 of read '57' because it was < 2 characters long 913s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 913s Warning: skipping read '79' because it was < 2 characters long 913s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 913s Warning: skipping mate #2 of read '85' because it was < 2 characters long 913s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '93' because it was < 2 characters long 913s 99 reads; of these: 913s 94 (94.95%) were paired; of these: 913s 94 (100.00%) aligned concordantly 0 times 913s 0 (0.00%) aligned concordantly exactly 1 time 913s 0 (0.00%) aligned concordantly >1 times 913s ---- 913s 94 pairs aligned concordantly 0 times; of these: 913s 0 (0.00%) aligned discordantly 1 time 913s ---- 913s 94 pairs aligned 0 times concordantly or discordantly; of these: 913s 188 mates make up the pairs; of these: 913s 188 (100.00%) aligned 0 times 913s 0 (0.00%) aligned exactly 1 time 913s 0 (0.00%) aligned >1 times 913s 5 (5.05%) were unpaired; of these: 913s 5 (100.00%) aligned 0 times 913s 0 (0.00%) aligned exactly 1 time 913s 0 (0.00%) aligned >1 times 913s 0.00% overall alignment rate 913s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 913s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 913s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 913s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 913s /usr/bin/bowtie2 --cp-min 4 --cp-ival 1 --mm --local --rdg 41.5437350511632,3.91235032470421 --np 2 --norc --trim5 4 --score-min L,5.34202035333576,3.71272648339241 -r -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 913s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 913s Warning: skipping mate #2 of read '5' because it was < 2 characters long 913s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '14' because it was < 2 characters long 913s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '25' because it was < 2 characters long 913s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '30' because it was < 2 characters long 913s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 913s Warning: skipping mate #2 of read '57' because it was < 2 characters long 913s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '40' because it was < 2 characters long 913s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '42' because it was < 2 characters long 913s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '67' because it was < 2 characters long 913s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 913s Warning: skipping mate #2 of read '85' because it was < 2 characters long 913s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 913s Warning: skipping read '79' because it was < 2 characters long 913s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 913s Warning: skipping mate #1 of read '93' because it was < 2 characters long 913s 99 reads; of these: 913s 94 (94.95%) were paired; of these: 913s 94 (100.00%) aligned concordantly 0 times 913s 0 (0.00%) aligned concordantly exactly 1 time 913s 0 (0.00%) aligned concordantly >1 times 913s ---- 913s 94 pairs aligned concordantly 0 times; of these: 913s 0 (0.00%) aligned discordantly 1 time 913s ---- 913s 94 pairs aligned 0 times concordantly or discordantly; of these: 913s 188 mates make up the pairs; of these: 913s 188 (100.00%) aligned 0 times 913s 0 (0.00%) aligned exactly 1 time 913s 0 (0.00%) aligned >1 times 913s 5 (5.05%) were unpaired; of these: 913s 5 (100.00%) aligned 0 times 913s 0 (0.00%) aligned exactly 1 time 913s 0 (0.00%) aligned >1 times 913s 0.00% overall alignment rate 913s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 913s Flattened IUPAC characters 913s Mutating sequence Sim.pm.2 913s Introducing 10 SNPs, 0/0 ref/read gaps, and 2 rearrangements 913s Finished SNPs 913s Finished ref gaps 913s Finished read gaps 913s Mutating sequence Sim.pm.1 913s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 913s Finished SNPs 913s Finished ref gaps 913s Finished read gaps 913s Mutated reference genome to subject genome 913s SNPs introduced: 10 913s Reference gaps introduced: 1 913s Read gaps introduced: 0 913s Rearrangements introduced: 3 913s Created read sampler 913s Sampling 70 reads 913s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 913s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 913s parsing sequence Sim.pm.1... 913s parsing sequence Sim.pm.2... 913s Parsed 74 reference bases 913s *** Run 59 of 100 913s /usr/bin/bowtie2 -N 1 -L22 --nofw --score-min L,9.16830215477649,2.84672444498706 -i S,0.777155110173945,0.946209374548773 --rfg 5.19573235401756,18.0510049403344 --trim5 0 --cp-ival 1 --cp-min 2 -k 7 --ma 24.2146499181377 --mp 9.56615914549843,7.86257618401152 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq 913s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 70 reads; of these: 913s 70 (100.00%) were unpaired; of these: 913s 59 (84.29%) aligned 0 times 913s 9 (12.86%) aligned exactly 1 time 913s 2 (2.86%) aligned >1 times 913s 15.71% overall alignment rate 913s Read 50 alignments... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s TACATGACTCTTTACA 913s TACATGACTCTTTACA 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s AAGAGGCGGGGTAA 913s AAGAGGCGGGGTAA 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s GAGGGCGATAAGGGCCGAA 913s GAGGGCGATAAGGGCCGAA 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s CG 913s CG 913s Processing line... 913s CG 913s CG 913s Processing line... 913s CG 913s CG 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s TTACACAAAGAGGCGGGGTAA 913s TTACACAAAGAGGCGGGGTAA 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s ACATGACTCTTT 913s ACATGACTCTTT 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s GCC 913s GCC 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s AC 913s AC 913s Processing line... 913s AC 913s AC 913s Processing line... 913s AC 913s AC 913s Processing line... 913s AC 913s AC 913s Processing line... 913s AC 913s AC 913s Processing line... 913s AC 913s AC 913s Processing line... 913s AC 913s AC 913s Processing line... 913s AGGGCGAT 913s AGGGCGAT 913s Processing line... 913s Processing line... 913s TACACAAA 913s TACACAAA 913s Processing line... 913s Processing line... 913s Processing line... 913s Processing line... 913s GGTGTACATG 913s GGTGTACATG 913s Processing line... 913s Processing line... 913s --- Summary --- 913s Read 1 reference strings 913s Checked 19 alignments, 0 edits 913s --------------- 913s PASSED 913s ALSO checking that bowtie2 and bowtie2-align match up 913s /usr/bin/bowtie2 -N 1 -L22 --nofw --score-min L,9.16830215477649,2.84672444498706 -i S,0.777155110173945,0.946209374548773 --rfg 5.19573235401756,18.0510049403344 --trim5 0 --cp-ival 1 --cp-min 2 -k 7 --ma 24.2146499181377 --mp 9.56615914549843,7.86257618401152 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 913s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 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 913s 70 reads; of these: 913s 70 (100.00%) were unpaired; of these: 913s 59 (84.29%) aligned 0 times 913s 9 (12.86%) aligned exactly 1 time 913s 2 (2.86%) aligned >1 times 913s 15.71% overall alignment rate 913s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 913s /usr/bin/bowtie2 -N 1 -L22 --nofw --score-min L,9.16830215477649,2.84672444498706 -i S,0.777155110173945,0.946209374548773 --rfg 5.19573235401756,18.0510049403344 --trim5 0 --cp-ival 1 --cp-min 2 -k 7 --ma 24.2146499181377 --mp 9.56615914549843,7.86257618401152 --qseq -p 3 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 913s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 914s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 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 914s 70 reads; of these: 914s 70 (100.00%) were unpaired; of these: 914s 59 (84.29%) aligned 0 times 914s 9 (12.86%) aligned exactly 1 time 914s 2 (2.86%) aligned >1 times 914s 15.71% overall alignment rate 914s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 914s Flattened IUPAC characters 914s Mutating sequence Sim.pm.1 914s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 914s Finished SNPs 914s Finished ref gaps 914s Finished read gaps 914s Mutating sequence Sim.pm.2 914s Introducing 7 SNPs, 1/1 ref/read gaps, and 0 rearrangements 914s Finished SNPs 914s Finished ref gaps 914s Finished read gaps 914s Mutated reference genome to subject genome 914s SNPs introduced: 10 914s Reference gaps introduced: 1 914s Read gaps introduced: 1 914s Rearrangements introduced: 0 914s Created read sampler 914s Sampling 124 reads 914s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 914s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 914s parsing sequence Sim.pm.1... 914s parsing sequence Sim.pm.2... 914s Parsed 74 reference bases 914s *** Run 60 of 100 914s /usr/bin/bowtie2 --rfg 26.4772448267629,17.568147480624 --mp 9.29126081092151,8.88764877591755 --score-min L,6.77837748972796,1.85438906616674 --ma 18.6780694917012 --np 9 --cp-min 5 -R 1 --cp-ival 2 --mm -N 1 -L22 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 914s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 914s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 914s Warning: skipping read '19' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '19' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 914s Warning: skipping read '21' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '21' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 914s Warning: skipping read '34' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '34' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 914s Warning: skipping read '39' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '39' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 914s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '48' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 914s Warning: skipping read '61' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '61' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 914s Warning: skipping read '80' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '80' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 914s 124 reads; of these: 914s 124 (100.00%) were unpaired; of these: 914s 103 (83.06%) aligned 0 times 914s 15 (12.10%) aligned exactly 1 time 914s 6 (4.84%) aligned >1 times 914s 16.94% overall alignment rate 914s Read 50 alignments... 914s Read 100 alignments... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s AC 914s AC 914s Processing line... 914s Processing line... 914s Processing line... 914s CCA 914s CCA 914s Processing line... 914s Processing line... 914s CCA 914s CCA 914s Processing line... 914s Processing line... 914s GGCGATAAGG 914s GGCGATAAGG 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s AGGCGG 914s AGGCGG 914s Processing line... 914s TGTACATGACTCTTTACACA 914s TGTACATGACTCTTTACACA 914s Processing line... 914s ACAA 914s ACAA 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s CCA 914s CCA 914s Processing line... 914s TCTTTACACAA 914s TCTTTACACAA 914s Processing line... 914s Processing line... 914s GGCGATA 914s GGCGATA 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s CATGACTCT 914s CATGACTCT 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s ACATGACT 914s ACATGACT 914s /usr/bin/bowtie2 --rfg 26.4772448267629,17.568147480624 --mp 9.29126081092151,8.88764877591755 --score-min L,6.77837748972796,1.85438906616674 --ma 18.6780694917012 --np 9 --cp-min 5 -R 1 --cp-ival 2 --mm -N 1 -L22 -f -p 2 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 914s Processing line... 914s CAT 914s CAT 914s Processing line... 914s Processing line... 914s Processing line... 914s GGCCG 914s GGCCG 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s GG 914s GG 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s AGG 914s AGG 914s Processing line... 914s Processing line... 914s ACA 914s ACA 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s AT 914s AT 914s Processing line... 914s Processing line... 914s Processing line... 914s ATGACTCTTTACACAAAGAGGCGGGG 914s ATGACTCTTTACACAAAGAGGCGGGG 914s Processing line... 914s Processing line... 914s AGAGGCGGGGT 914s AGAGGCGGGGT 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s Processing line... 914s GCGGGG 914s GCGGGG 914s --- Summary --- 914s Read 1 reference strings 914s Checked 21 alignments, 0 edits 914s --------------- 914s PASSED 914s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 914s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 914s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 914s Warning: skipping read '19' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '19' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 914s Warning: skipping read '21' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '21' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 914s Warning: skipping read '34' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '34' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 914s Warning: skipping read '39' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '39' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 914s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '48' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 914s Warning: skipping read '61' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '61' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 914s Warning: skipping read '80' because length (1) <= # seed mismatches (1) 914s Warning: skipping read '80' because it was < 2 characters long 914s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 914s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 914s 124 reads; of these: 914s 124 (100.00%) were unpaired; of these: 914s 103 (83.06%) aligned 0 times 914s 15 (12.10%) aligned exactly 1 time 914s 6 (4.84%) aligned >1 times 914s 16.94% overall alignment rate 914s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 914s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 914s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 914s Flattened IUPAC characters 914s Mutating sequence Sim.pm.1 914s Introducing 5 SNPs, 0/1 ref/read gaps, and 1 rearrangements 914s Finished SNPs 914s Finished ref gaps 914s Finished read gaps 914s Mutating sequence Sim.pm.2 914s Introducing 14 SNPs, 0/0 ref/read gaps, and 0 rearrangements 914s Finished SNPs 914s Finished ref gaps 914s Finished read gaps 914s Mutated reference genome to subject genome 914s SNPs introduced: 19 914s Reference gaps introduced: 0 914s Read gaps introduced: 1 914s Rearrangements introduced: 1 914s Created read sampler 914s Sampling 109 reads 914s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 914s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 914s parsing sequence Sim.pm.1... 914s parsing sequence Sim.pm.2... 914s Parsed 74 reference bases 914s *** Run 61 of 100 914s /usr/bin/bowtie2 --cp-ival 1 -R 1 --cp-min 6 --np 1 -M 3 --score-min L,3.22344151232044,7.93830414244712 --mp 8.58514793624057,6.77813417564212 --rdg 11.1133661124092,11.0843182230215 -i S,2.03597380596109,5.97422127882429 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 915s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 915s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 915s Warning: skipping mate #2 of read '4' because it was < 2 characters long 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 915s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 915s Warning: skipping mate #2 of read '5' because it was < 2 characters long 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 915s Warning: skipping mate #1 of read '33' because length (1) <= # seed mismatches (0) 915s Warning: skipping mate #1 of read '33' because it was < 2 characters long 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 915s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 915s Warning: skipping mate #1 of read '36' because it was < 2 characters long 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 915s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 915s Warning: skipping mate #2 of read '48' because it was < 2 characters long 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 915s Read 50 alignments... 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 915s Read 100 alignments... 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 915s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (0) 915s Warning: skipping mate #1 of read '84' because it was < 2 characters long 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 915s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (0) 915s Warning: skipping mate #2 of read '88' because it was < 2 characters long 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 915s Warning: skipping mate #2 of read '104' because length (1) <= # seed mismatches (0) 915s Warning: skipping mate #2 of read '104' because it was < 2 characters long 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 915s Warning: skipping mate #2 of read '105' because length (1) <= # seed mismatches (0) 915s Warning: skipping mate #2 of read '105' because it was < 2 characters long 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 915s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 915s 109 reads; of these: 915s 109 (100.00%) were paired; of these: 915s 106 (97.25%) aligned concordantly 0 times 915s 2 (1.83%) aligned concordantly exactly 1 time 915s 1 (0.92%) aligned concordantly >1 times 915s ---- 915s 106 pairs aligned concordantly 0 times; of these: 915s 0 (0.00%) aligned discordantly 1 time 915s ---- 915s 106 pairs aligned 0 times concordantly or discordantly; of these: 915s 212 mates make up the pairs; of these: 915s 189 (89.15%) aligned 0 times 915s 13 (6.13%) aligned exactly 1 time 915s 10 (4.72%) aligned >1 times 915s 13.30% overall alignment rate 915s Read 150 alignments... 915s Read 200 alignments... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s CA 915s CA 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s GGG 915s GGG 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s TA 915s TA 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s ACATTCAGC 915s ACATTCAGC 915s Processing line... 915s GACT 915s GACT 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s TTCAGCTACC 915s TTCAGCTACC 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s AAAGAGGCGGGGTAA 915s AAAGAGGCGGGGTAA 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s TTTACACA 915s TTTACACA 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s TTACA 915s TTACA 915s Processing line... 915s Processing line... 915s TGTACATGAC 915s TGTACATGAC 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s GCTACCA 915s GCTACCA 915s Processing line... 915s Processing line... 915s AG 915s AG 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s GTG 915s GTG 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s CAA 915s CAA 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s AAGA 915s AAGA 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s GGTGTACATGACTCTTTAC 915s GGTGTACATGACTCTTTAC 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s GGG 915s GGG 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s CTCTT 915s CTCTT 915s Processing line... 915s Processing line... 915s ATG 915s ATG 915s Processing line... 915s Processing line... 915s AACATTCA 915s AACATTCA 915s Processing line... 915s Processing line... 915s CA 915s CA 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s TAACATTCAGCTA 915s TAACATTCAGCTA 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s CAG 915s CAG 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s AGAGGCG 915s AGAGGCG 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s GGGTAACATT 915s GGGTAACATT 915s Processing line... 915s ATTCAGCTACCA 915s ATTCAGCTACCA 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s GTGTAC 915s GTGTAC 915s Processing line... 915s AA 915s AA 915s Processing line... 915s CCA 915s CCA 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s --- Summary --- 915s Read 1 reference strings 915s Checked 29 alignments, 0 edits 915s --------------- 915s PASSED 915s Flattened IUPAC characters 915s Mutating sequence Sim.pm.2 915s Introducing 13 SNPs, 0/0 ref/read gaps, and 0 rearrangements 915s Finished SNPs 915s Finished ref gaps 915s Finished read gaps 915s Mutating sequence Sim.pm.1 915s Introducing 3 SNPs, 2/0 ref/read gaps, and 0 rearrangements 915s Finished SNPs 915s Finished ref gaps 915s Finished read gaps 915s Mutated reference genome to subject genome 915s SNPs introduced: 16 915s Reference gaps introduced: 2 915s Read gaps introduced: 0 915s Rearrangements introduced: 0 915s Created read sampler 915s Sampling 13 reads 915s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 915s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 915s parsing sequence Sim.pm.1... 915s parsing sequence Sim.pm.2... 915s Parsed 74 reference bases 915s *** Run 62 of 100 915s /usr/bin/bowtie2 -R 1 --np 2 --score-min L,5.79231309487792,9.50679393255966 --rfg 29.8674259147286 -i L,0.274866867747011 --cp-ival 2 --cp-min 9 -M 2 --mp 4.79639833313127,4.62332824896225 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq 915s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 915s 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 915s 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 915s 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 915s 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 915s 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 915s 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 915s 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 915s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 915s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 915s 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 915s 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 915s 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 915s 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 915s 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 915s 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 915s 13 reads; of these: 915s 13 (100.00%) were unpaired; of these: 915s 12 (92.31%) aligned 0 times 915s 1 (7.69%) aligned exactly 1 time 915s 0 (0.00%) aligned >1 times 915s 7.69% overall alignment rate 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s Processing line... 915s GGAGGGCGATAAGGGCCGAAC 915s GGAGGGCGATAAGGGCCGAAC 915s Processing line... 915s Processing line... 915s Processing line... 915s --- Summary --- 915s Read 1 reference strings 915s Checked 1 alignments, 0 edits 915s --------------- 915s PASSED 915s ALSO checking that bowtie2 and bowtie2-align match up 915s /usr/bin/bowtie2 -R 1 --np 2 --score-min L,5.79231309487792,9.50679393255966 --rfg 29.8674259147286 -i L,0.274866867747011 --cp-ival 2 --cp-min 9 -M 2 --mp 4.79639833313127,4.62332824896225 --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 915s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 915s 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 915s 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 915s 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 915s 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 915s 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 915s 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 915s 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 915s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 915s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 915s 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 915s 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 915s 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 915s 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 915s 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 915s 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 915s 13 reads; of these: 915s 13 (100.00%) were unpaired; of these: 915s 12 (92.31%) aligned 0 times 915s 1 (7.69%) aligned exactly 1 time 915s 0 (0.00%) aligned >1 times 915s 7.69% overall alignment rate 915s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 915s Flattened IUPAC characters 915s Mutating sequence Sim.pm.1 915s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 915s Finished SNPs 915s Finished ref gaps 915s Finished read gaps 915s Mutating sequence Sim.pm.2 915s Introducing 8 SNPs, 0/2 ref/read gaps, and 2 rearrangements 915s Finished SNPs 915s Finished ref gaps 915s Finished read gaps 915s Mutated reference genome to subject genome 915s SNPs introduced: 15 915s Reference gaps introduced: 0 915s Read gaps introduced: 2 915s Rearrangements introduced: 3 915s Created read sampler 915s Sampling 48 reads 915s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 915s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 915s parsing sequence Sim.pm.1... 915s parsing sequence Sim.pm.2... 915s Parsed 74 reference bases 915s *** Run 63 of 100 915s /usr/bin/bowtie2 --score-min L,9.29478053984062,3.04408723849217 -M 3 --rfg 34.4812440261737,2.83708604339152 --local --trim5 3 --cp-ival 4 --cp-min 3 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 915s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 915s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 915s Warning: skipping read '2' because it was < 2 characters long 915s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 915s Warning: skipping read '12' because it was < 2 characters long 915s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 915s Warning: skipping read '16' because it was < 2 characters long 915s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 916s Warning: skipping read '41' because it was < 2 characters long 916s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 916s Warning: skipping read '43' because it was < 2 characters long 916s 48 reads; of these: 916s 48 (100.00%) were unpaired; of these: 916s 48 (100.00%) aligned 0 times 916s 0 (0.00%) aligned exactly 1 time 916s 0 (0.00%) aligned >1 times 916s 0.00% overall alignment rate 916s Read 50 alignments... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s --- Summary --- 916s Read 1 reference strings 916s Checked 0 alignments, 0 edits 916s --------------- 916s PASSED 916s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 916s /usr/bin/bowtie2 --score-min L,9.29478053984062,3.04408723849217 -M 3 --rfg 34.4812440261737,2.83708604339152 --local --trim5 3 --cp-ival 4 --cp-min 3 -f -p 3 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 916s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 916s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 916s Warning: skipping read '2' because it was < 2 characters long 916s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 916s Warning: skipping read '12' because it was < 2 characters long 916s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 916s Warning: skipping read '16' because it was < 2 characters long 916s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 916s Warning: skipping read '41' because it was < 2 characters long 916s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 916s Warning: skipping read '43' because it was < 2 characters long 916s 48 reads; of these: 916s 48 (100.00%) were unpaired; of these: 916s 48 (100.00%) aligned 0 times 916s 0 (0.00%) aligned exactly 1 time 916s 0 (0.00%) aligned >1 times 916s 0.00% overall alignment rate 916s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 916s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 916s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 916s Flattened IUPAC characters 916s Mutating sequence Sim.pm.1 916s Introducing 1 SNPs, 0/0 ref/read gaps, and 2 rearrangements 916s Finished SNPs 916s Finished ref gaps 916s Finished read gaps 916s Mutating sequence Sim.pm.2 916s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 916s Finished SNPs 916s Finished ref gaps 916s Finished read gaps 916s Mutated reference genome to subject genome 916s SNPs introduced: 10 916s Reference gaps introduced: 0 916s Read gaps introduced: 0 916s Rearrangements introduced: 2 916s Created read sampler 916s Sampling 40 reads 916s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 916s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 916s parsing sequence Sim.pm.1... 916s parsing sequence Sim.pm.2... 916s Parsed 74 reference bases 916s *** Run 64 of 100 916s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --np 1 -k 3 --score-min L,6.02289299478098,1.97952422604876 --mp 8.90143849077741,2.14223332195069 --local --rfg 13.0229048412046,8.21863216701138 -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 916s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 916s Warning: skipping read '10' because it was < 2 characters long 916s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 916s Warning: skipping read '28' because it was < 2 characters long 916s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 916s Warning: skipping read '37' because it was < 2 characters long 916s 40 reads; of these: 916s 40 (100.00%) were unpaired; of these: 916s 40 (100.00%) aligned 0 times 916s 0 (0.00%) aligned exactly 1 time 916s 0 (0.00%) aligned >1 times 916s 0.00% overall alignment rate 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s Processing line... 916s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --np 1 -k 3 --score-min L,6.02289299478098,1.97952422604876 --mp 8.90143849077741,2.14223332195069 --local --rfg 13.0229048412046,8.21863216701138 -r -p 3 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 916s Processing line... 916s --- Summary --- 916s Read 1 reference strings 916s Checked 0 alignments, 0 edits 916s --------------- 916s PASSED 916s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 916s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 916s Warning: skipping read '10' because it was < 2 characters long 916s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 916s Warning: skipping read '28' because it was < 2 characters long 916s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 916s Warning: skipping read '37' because it was < 2 characters long 916s 40 reads; of these: 916s 40 (100.00%) were unpaired; of these: 916s 40 (100.00%) aligned 0 times 916s 0 (0.00%) aligned exactly 1 time 916s 0 (0.00%) aligned >1 times 916s 0.00% overall alignment rate 916s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 916s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 916s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 916s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 916s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --np 1 -k 3 --score-min L,6.02289299478098,1.97952422604876 --mp 8.90143849077741,2.14223332195069 --local --rfg 13.0229048412046,8.21863216701138 -r -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 917s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 917s Warning: skipping read '10' because it was < 2 characters long 917s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 917s Warning: skipping read '28' because it was < 2 characters long 917s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 917s Warning: skipping read '37' because it was < 2 characters long 917s 40 reads; of these: 917s 40 (100.00%) were unpaired; of these: 917s 40 (100.00%) aligned 0 times 917s 0 (0.00%) aligned exactly 1 time 917s 0 (0.00%) aligned >1 times 917s 0.00% overall alignment rate 917s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 917s Flattened IUPAC characters 917s Mutating sequence Sim.pm.1 917s Introducing 6 SNPs, 4/0 ref/read gaps, and 0 rearrangements 917s Finished SNPs 917s Finished ref gaps 917s Finished read gaps 917s Mutating sequence Sim.pm.2 917s Introducing 8 SNPs, 2/0 ref/read gaps, and 0 rearrangements 917s Finished SNPs 917s Finished ref gaps 917s Finished read gaps 917s Mutated reference genome to subject genome 917s SNPs introduced: 14 917s Reference gaps introduced: 6 917s Read gaps introduced: 0 917s Rearrangements introduced: 0 917s Created read sampler 917s Sampling 44 reads 917s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 917s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 917s parsing sequence Sim.pm.1... 917s parsing sequence Sim.pm.2... 917s Parsed 74 reference bases 917s *** Run 65 of 100 917s /usr/bin/bowtie2 --local --mp 9.5755821023716,1.96716966908864 --cp-min 3 --cp-ival 2 --mm --score-min L,9.1215649877363,1.81157764326041 --n-ceil 1.00007065898087,0.444262305629578 -R 3 -N 1 -L17 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 917s Warning: skipping read '29' because length (1) <= # seed mismatches (1) 917s Warning: skipping read '29' because it was < 2 characters long 917s 44 reads; of these: 917s 44 (100.00%) were unpaired; of these: 917s 44 (100.00%) aligned 0 times 917s 0 (0.00%) aligned exactly 1 time 917s 0 (0.00%) aligned >1 times 917s 0.00% overall alignment rate 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s Processing line... 917s --- Summary --- 917s Read 1 reference strings 917s Checked 0 alignments, 0 edits 917s /usr/bin/bowtie2 --local --mp 9.5755821023716,1.96716966908864 --cp-min 3 --cp-ival 2 --mm --score-min L,9.1215649877363,1.81157764326041 --n-ceil 1.00007065898087,0.444262305629578 -R 3 -N 1 -L17 -q -p 4 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 917s --------------- 917s PASSED 917s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 917s Warning: skipping read '29' because length (1) <= # seed mismatches (1) 917s Warning: skipping read '29' because it was < 2 characters long 917s 44 reads; of these: 917s 44 (100.00%) were unpaired; of these: 917s 44 (100.00%) aligned 0 times 917s 0 (0.00%) aligned exactly 1 time 917s 0 (0.00%) aligned >1 times 917s 0.00% overall alignment rate 917s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 917s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 917s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 917s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 917s /usr/bin/bowtie2 --local --mp 9.5755821023716,1.96716966908864 --cp-min 3 --cp-ival 2 --mm --score-min L,9.1215649877363,1.81157764326041 --n-ceil 1.00007065898087,0.444262305629578 -R 3 -N 1 -L17 -q -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 917s Warning: skipping read '29' because length (1) <= # seed mismatches (1) 917s Warning: skipping read '29' because it was < 2 characters long 917s 44 reads; of these: 917s 44 (100.00%) were unpaired; of these: 917s 44 (100.00%) aligned 0 times 917s 0 (0.00%) aligned exactly 1 time 917s 0 (0.00%) aligned >1 times 917s 0.00% overall alignment rate 917s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 918s Flattened IUPAC characters 918s Mutating sequence Sim.pm.2 918s Introducing 16 SNPs, 1/0 ref/read gaps, and 2 rearrangements 918s Finished SNPs 918s Finished ref gaps 918s Finished read gaps 918s Mutating sequence Sim.pm.1 918s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 918s Finished SNPs 918s Finished ref gaps 918s Finished read gaps 918s Mutated reference genome to subject genome 918s SNPs introduced: 18 918s Reference gaps introduced: 1 918s Read gaps introduced: 1 918s Rearrangements introduced: 2 918s Created read sampler 918s Sampling 176 reads 918s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 918s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 918s parsing sequence Sim.pm.1... 918s parsing sequence Sim.pm.2... 918s Parsed 74 reference bases 918s *** Run 66 of 100 918s /usr/bin/bowtie2 --cp-min 10 --cp-ival 3 --trim3 3 --rdg 3.30969885984641 --ma 12.9902582569849 --norc -D 33 --trim5 7 --n-ceil 1.09420032101079,0.610485853343875 --score-min L,8.03021578796596,6.3241883155685 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 918s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 918s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '2' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 918s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '6' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 918s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '11' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 918s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '14' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 918s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '23' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 918s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '27' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 918s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '35' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 918s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '37' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 918s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '41' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 918s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '45' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 918s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '48' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 918s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #2 of read '53' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 918s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '54' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 918s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '57' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 918s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '58' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 918s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '59' because it was < 2 characters long 918s Warning: skipping mate #2 of read '59' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 918s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '60' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 918s Read 50 alignments... 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 918s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '69' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 918s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '70' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 918s Read 100 alignments... 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 918s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '76' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 918s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '81' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 918s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '89' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 918s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '91' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 918s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '104' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 918s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '109' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 918s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '119' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 918s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '128' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 918s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '131' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 918s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '135' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 918s Read 150 alignments... 918s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 918s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '152' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 918s Warning: skipping mate #1 of read '157' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '157' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 918s 176 reads; of these: 918s 141 (80.11%) were paired; of these: 918s 141 (100.00%) aligned concordantly 0 times 918s 0 (0.00%) aligned concordantly exactly 1 time 918s 0 (0.00%) aligned concordantly >1 times 918s ---- 918s 141 pairs aligned concordantly 0 times; of these: 918s 0 (0.00%) aligned discordantly 1 time 918s ---- 918s 141 pairs aligned 0 times concordantly or discordantly; of these: 918s 282 mates make up the pairs; of these: 918s 263 (93.26%) aligned 0 times 918s 15 (5.32%) aligned exactly 1 time 918s 4 (1.42%) aligned >1 times 918s 35 (19.89%) were unpaired; of these: 918s 33 (94.29%) aligned 0 times 918s 2 (5.71%) aligned exactly 1 time 918s 0 (0.00%) aligned >1 times 918s 6.62% overall alignment rate 918s Read 200 alignments... 918s Read 250 alignments... 918s Read 300 alignments... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s GGG 918s GGG 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s GTGT 918s GTGT 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s ATGACTCTTTACAC 918s ATGACTCTTTACAC 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s TGA 918s TGA 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s CACAAAGAGGCGGGG 918s CACAAAGAGGCGGGG 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s TTAC 918s TTAC 918s Processing line... 918s Processing line... 918s CTCTTTACACAAAGAGGCGG 918s CTCTTTACACAAAGAGGCGG 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s TCAGCTACCA 918s TCAGCTACCA 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s ACTCTTTACACAAAGAG 918s ACTCTTTACACAAAGAG 918s Processing line... 918s Processing line... 918s ACATGACTCTTTACACAAAGAG 918s ACATGACTCTTTACACAAAGAG 918s Processing line... 918s Processing line... 918s TACACAAAGAGGCG 918s TACACAAAGAGGCG 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s CATGACTCTTTACACAAAG 918s CATGACTCTTTACACAAAG 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s TGTA 918s TGTA 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s GTACATGACTC 918s GTACATGACTC 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s AC 918s AC 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s ACAAAGAGGCGG 918s ACAAAGAGGCGG 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s CAGC 918s CAGC 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s TACACAAAGAGGCG 918s TACACAAAGAGGCG 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s TA 918s TA 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s Processing line... 918s TAC 918s TAC 918s Processing line... 918s Processing line... 918s TACAT 918s TACAT 918s Processing line... 918s Processing line... 918s Processing line... 918s --- Summary --- 918s Read 1 reference strings 918s Checked 21 alignments, 0 edits 918s --------------- 918s PASSED 918s ALSO checking that bowtie2 and bowtie2-align match up 918s /usr/bin/bowtie2 --cp-min 10 --cp-ival 3 --trim3 3 --rdg 3.30969885984641 --ma 12.9902582569849 --norc -D 33 --trim5 7 --n-ceil 1.09420032101079,0.610485853343875 --score-min L,8.03021578796596,6.3241883155685 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 918s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 918s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '2' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 918s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '6' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 918s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '11' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 918s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '14' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 918s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '23' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 918s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '27' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 918s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '35' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 918s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '37' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 918s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '41' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 918s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '45' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 918s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '48' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 918s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #2 of read '53' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 918s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '54' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 918s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '57' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 918s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '58' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 918s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '59' because it was < 2 characters long 918s Warning: skipping mate #2 of read '59' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 918s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '60' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 918s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '69' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 918s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '70' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 918s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '76' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 918s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '81' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 918s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '89' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 918s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '91' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 918s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '104' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 918s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '109' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 918s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '119' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 918s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '128' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 918s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '131' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 918s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '135' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 918s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 918s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '152' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 918s Warning: skipping mate #1 of read '157' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '157' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 918s 176 reads; of these: 918s 141 (80.11%) were paired; of these: 918s 141 (100.00%) aligned concordantly 0 times 918s 0 (0.00%) aligned concordantly exactly 1 time 918s 0 (0.00%) aligned concordantly >1 times 918s ---- 918s 141 pairs aligned concordantly 0 times; of these: 918s 0 (0.00%) aligned discordantly 1 time 918s ---- 918s 141 pairs aligned 0 times concordantly or discordantly; of these: 918s 282 mates make up the pairs; of these: 918s 263 (93.26%) aligned 0 times 918s 15 (5.32%) aligned exactly 1 time 918s 4 (1.42%) aligned >1 times 918s 35 (19.89%) were unpaired; of these: 918s 33 (94.29%) aligned 0 times 918s 2 (5.71%) aligned exactly 1 time 918s 0 (0.00%) aligned >1 times 918s 6.62% overall alignment rate 918s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 918s /usr/bin/bowtie2 --cp-min 10 --cp-ival 3 --trim3 3 --rdg 3.30969885984641 --ma 12.9902582569849 --norc -D 33 --trim5 7 --n-ceil 1.09420032101079,0.610485853343875 --score-min L,8.03021578796596,6.3241883155685 -f -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 918s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 918s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '2' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 918s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '6' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 918s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '11' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 918s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '14' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 918s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '35' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 918s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '37' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 918s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '41' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 918s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '23' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 918s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '27' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 918s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '45' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 918s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '48' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 918s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #2 of read '53' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 918s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '54' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 918s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '57' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 918s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '58' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 918s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '59' because it was < 2 characters long 918s Warning: skipping mate #2 of read '59' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 918s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '60' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 918s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '81' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 918s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '89' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 918s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '91' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 918s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '69' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 918s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '70' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 918s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '76' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 918s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '119' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 918s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '104' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 918s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 918s Warning: skipping mate #1 of read '109' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 918s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 918s Warning: skipping read '131' because it was < 2 characters long 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 918s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 919s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '128' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 919s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 919s Warning: skipping read '152' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 919s Warning: skipping mate #1 of read '157' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '157' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 919s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 919s Warning: skipping read '135' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 919s 176 reads; of these: 919s 141 (80.11%) were paired; of these: 919s 141 (100.00%) aligned concordantly 0 times 919s 0 (0.00%) aligned concordantly exactly 1 time 919s 0 (0.00%) aligned concordantly >1 times 919s ---- 919s 141 pairs aligned concordantly 0 times; of these: 919s 0 (0.00%) aligned discordantly 1 time 919s ---- 919s 141 pairs aligned 0 times concordantly or discordantly; of these: 919s 282 mates make up the pairs; of these: 919s 263 (93.26%) aligned 0 times 919s 15 (5.32%) aligned exactly 1 time 919s 4 (1.42%) aligned >1 times 919s 35 (19.89%) were unpaired; of these: 919s 33 (94.29%) aligned 0 times 919s 2 (5.71%) aligned exactly 1 time 919s 0 (0.00%) aligned >1 times 919s 6.62% overall alignment rate 919s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 919s Flattened IUPAC characters 919s Mutating sequence Sim.pm.2 919s Introducing 12 SNPs, 0/0 ref/read gaps, and 1 rearrangements 919s Finished SNPs 919s Finished ref gaps 919s Finished read gaps 919s Mutating sequence Sim.pm.1 919s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 919s Finished SNPs 919s Finished ref gaps 919s Finished read gaps 919s Mutated reference genome to subject genome 919s SNPs introduced: 15 919s Reference gaps introduced: 1 919s Read gaps introduced: 0 919s Rearrangements introduced: 1 919s Created read sampler 919s Sampling 53 reads 919s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 919s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 919s *** Run 67 of 100 919s /usr/bin/bowtie2 --trim5 6 --score-min L,1.16902303712767,9.13296086029228 --np 3 -R 1 --rdg 9.23095374024989,1.84874052188496 --trim3 4 --local -M 5 --cp-min 2 --mm --cp-ival 1 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq 919s parsing sequence Sim.pm.1... 919s parsing sequence Sim.pm.2... 919s Parsed 74 reference bases 919s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 919s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 919s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 919s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 919s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 919s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 919s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 919s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 919s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 919s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 919s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 919s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 919s Warning: skipping mate #2 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 919s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 919s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 919s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 919s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 919s 53 reads; of these: 919s 42 (79.25%) were paired; of these: 919s 42 (100.00%) aligned concordantly 0 times 919s 0 (0.00%) aligned concordantly exactly 1 time 919s 0 (0.00%) aligned concordantly >1 times 919s ---- 919s 42 pairs aligned concordantly 0 times; of these: 919s 0 (0.00%) aligned discordantly 1 time 919s ---- 919s 42 pairs aligned 0 times concordantly or discordantly; of these: 919s 84 mates make up the pairs; of these: 919s 84 (100.00%) aligned 0 times 919s 0 (0.00%) aligned exactly 1 time 919s 0 (0.00%) aligned >1 times 919s 11 (20.75%) were unpaired; of these: 919s 11 (100.00%) aligned 0 times 919s 0 (0.00%) aligned exactly 1 time 919s 0 (0.00%) aligned >1 times 919s 0.00% overall alignment rate 919s Read 50 alignments... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s --- Summary --- 919s Read 1 reference strings 919s Checked 0 alignments, 0 edits 919s --------------- 919s PASSED 919s Flattened IUPAC characters 919s Mutating sequence Sim.pm.2 919s Introducing 2 SNPs, 2/1 ref/read gaps, and 2 rearrangements 919s Finished SNPs 919s Finished ref gaps 919s Finished read gaps 919s Mutating sequence Sim.pm.1 919s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 919s Finished SNPs 919s Finished ref gaps 919s Finished read gaps 919s Mutated reference genome to subject genome 919s SNPs introduced: 3 919s Reference gaps introduced: 2 919s Read gaps introduced: 2 919s Rearrangements introduced: 2 919s Created read sampler 919s Sampling 51 reads 919s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 919s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 919s parsing sequence Sim.pm.1... 919s *** Run 68 of 100 919s /usr/bin/bowtie2 --cp-min 2 --cp-ival 2 --rfg 28.6622302594081 --mp 6.11779778870419,3.43856185454771 --trim5 6 --score-min L,6.68246037140914,6.3439443741158 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 919s parsing sequence Sim.pm.2... 919s Parsed 74 reference bases 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 919s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read '2' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 919s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '9' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 919s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '15' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 919s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read '17' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 919s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '29' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 919s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '31' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 919s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '34' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 919s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read '36' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 919s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '38' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 919s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read '39' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 919s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '40' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 919s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read '46' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 919s 51 reads; of these: 919s 44 (86.27%) were paired; of these: 919s 44 (100.00%) aligned concordantly 0 times 919s 0 (0.00%) aligned concordantly exactly 1 time 919s 0 (0.00%) aligned concordantly >1 times 919s ---- 919s 44 pairs aligned concordantly 0 times; of these: 919s 0 (0.00%) aligned discordantly 1 time 919s ---- 919s 44 pairs aligned 0 times concordantly or discordantly; of these: 919s 88 mates make up the pairs; of these: 919s 72 (81.82%) aligned 0 times 919s 13 (14.77%) aligned exactly 1 time 919s 3 (3.41%) aligned >1 times 919s 7 (13.73%) were unpaired; of these: 919s 5 (71.43%) aligned 0 times 919s 1 (14.29%) aligned exactly 1 time 919s 1 (14.29%) aligned >1 times 919s 18.95% overall alignment rate 919s Read 50 alignments... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s TACACAAAGAGGCGGGG 919s TACACAAAGAGGCGGGG 919s Processing line... 919s Processing line... 919s GACTCTTTACACAAAG 919s GACTCTTTACACAAAG 919s Processing line... 919s Processing line... 919s GG 919s GG 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s GGCG 919s GGCG 919s Processing line... 919s CT 919s CT 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s AAAGAGGCGGGGTAACATTCAG 919s AAAGAGGCGGGGTAACATTCAG 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s AAAGAGGCGGGGTAACATT 919s AAAGAGGCGGGGTAACATT 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s TC 919s TC 919s Processing line... 919s Processing line... 919s TGACTCTTT 919s TGACTCTTT 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s CATTC 919s CATTC 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s AGAGGCGGGGTAACA 919s AGAGGCGGGGTAACA 919s Processing line... 919s Processing line... 919s GGTAA 919s GGTAA 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s TGACTCTTTACACAAAGAGGCGGGGTAACAT 919s TGACTCTTTACACAAAGAGGCGGGGTAACAT 919s Processing line... 919s Processing line... 919s AAGAGG 919s AAGAGG 919s Processing line... 919s Processing line... 919s Processing line... 919s GGGTGTACATGACTCTTTAC 919s GGGTGTACATGACTCTTTAC 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s /usr/bin/bowtie2 --cp-min 2 --cp-ival 2 --rfg 28.6622302594081 --mp 6.11779778870419,3.43856185454771 --trim5 6 --score-min L,6.68246037140914,6.3439443741158 -f -p 4 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s GTACATGACTCTTTACACAAA 919s GTACATGACTCTTTACACAAA 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s TGACTC 919s TGACTC 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s Processing line... 919s CAAAGAGGCGGGGTAA 919s CAAAGAGGCGGGGTAA 919s Processing line... 919s Processing line... 919s Processing line... 919s --- Summary --- 919s Read 1 reference strings 919s Checked 18 alignments, 0 edits 919s --------------- 919s PASSED 919s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 919s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read '2' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 919s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read '17' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 919s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '9' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 919s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '15' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 919s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '29' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 919s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '31' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 919s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '34' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 919s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read '36' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 919s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '38' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 919s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read '39' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 919s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 919s Warning: skipping mate #1 of read '40' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 919s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 919s Warning: skipping mate #2 of read '46' because it was < 2 characters long 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 919s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 919s 51 reads; of these: 919s 44 (86.27%) were paired; of these: 919s 44 (100.00%) aligned concordantly 0 times 919s 0 (0.00%) aligned concordantly exactly 1 time 919s 0 (0.00%) aligned concordantly >1 times 919s ---- 919s 44 pairs aligned concordantly 0 times; of these: 919s 0 (0.00%) aligned discordantly 1 time 919s ---- 919s 44 pairs aligned 0 times concordantly or discordantly; of these: 919s 88 mates make up the pairs; of these: 919s 72 (81.82%) aligned 0 times 919s 13 (14.77%) aligned exactly 1 time 919s 3 (3.41%) aligned >1 times 919s 7 (13.73%) were unpaired; of these: 919s 5 (71.43%) aligned 0 times 919s 1 (14.29%) aligned exactly 1 time 919s 1 (14.29%) aligned >1 times 919s 18.95% overall alignment rate 919s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 919s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 919s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 919s /usr/bin/bowtie2 --cp-min 2 --cp-ival 2 --rfg 28.6622302594081 --mp 6.11779778870419,3.43856185454771 --trim5 6 --score-min L,6.68246037140914,6.3439443741158 -f -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 919s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 920s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 920s Warning: skipping mate #2 of read '2' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 920s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 920s Warning: skipping mate #2 of read '17' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 920s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 920s Warning: skipping mate #1 of read '9' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 920s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 920s Warning: skipping mate #1 of read '34' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 920s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 920s Warning: skipping mate #1 of read '15' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 920s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 920s Warning: skipping mate #2 of read '36' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 920s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 920s Warning: skipping mate #1 of read '38' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 920s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 920s Warning: skipping mate #2 of read '39' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 920s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 920s Warning: skipping mate #1 of read '40' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 920s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 920s Warning: skipping mate #2 of read '46' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 920s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 920s Warning: skipping mate #1 of read '29' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 920s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 920s Warning: skipping mate #1 of read '31' because it was < 2 characters long 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 920s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 920s 51 reads; of these: 920s 44 (86.27%) were paired; of these: 920s 44 (100.00%) aligned concordantly 0 times 920s 0 (0.00%) aligned concordantly exactly 1 time 920s 0 (0.00%) aligned concordantly >1 times 920s ---- 920s 44 pairs aligned concordantly 0 times; of these: 920s 0 (0.00%) aligned discordantly 1 time 920s ---- 920s 44 pairs aligned 0 times concordantly or discordantly; of these: 920s 88 mates make up the pairs; of these: 920s 72 (81.82%) aligned 0 times 920s 13 (14.77%) aligned exactly 1 time 920s 3 (3.41%) aligned >1 times 920s 7 (13.73%) were unpaired; of these: 920s 5 (71.43%) aligned 0 times 920s 1 (14.29%) aligned exactly 1 time 920s 1 (14.29%) aligned >1 times 920s 18.95% overall alignment rate 920s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 920s Flattened IUPAC characters 920s Mutating sequence Sim.pm.1 920s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 920s Finished SNPs 920s Finished ref gaps 920s Finished read gaps 920s Mutating sequence Sim.pm.2 920s Introducing 3 SNPs, 2/0 ref/read gaps, and 0 rearrangements 920s Finished SNPs 920s Finished ref gaps 920s Finished read gaps 920s Mutated reference genome to subject genome 920s SNPs introduced: 6 920s Reference gaps introduced: 2 920s Read gaps introduced: 0 920s Rearrangements introduced: 0 920s Created read sampler 920s Sampling 77 reads 920s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 920s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 920s parsing sequence Sim.pm.1... 920s parsing sequence Sim.pm.2... 920s Parsed 74 reference bases 920s *** Run 69 of 100 920s /usr/bin/bowtie2 --local --trim5 0 --score-min L,5.19834192928815,8.28188684534299 --np 1 --cp-min 2 --cp-ival 1 -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw 920s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 920s Warning: skipping mate #1 of read '34' because it was < 2 characters long 920s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 920s Warning: skipping mate #2 of read '40' because it was < 2 characters long 920s Read 50 alignments... 920s Read 100 alignments... 920s 77 reads; of these: 920s 77 (100.00%) were paired; of these: 920s 77 (100.00%) aligned concordantly 0 times 920s 0 (0.00%) aligned concordantly exactly 1 time 920s 0 (0.00%) aligned concordantly >1 times 920s ---- 920s 77 pairs aligned concordantly 0 times; of these: 920s 0 (0.00%) aligned discordantly 1 time 920s ---- 920s 77 pairs aligned 0 times concordantly or discordantly; of these: 920s 154 mates make up the pairs; of these: 920s 154 (100.00%) aligned 0 times 920s 0 (0.00%) aligned exactly 1 time 920s 0 (0.00%) aligned >1 times 920s 0.00% overall alignment rate 920s Read 150 alignments... 920s Processing line... 920s Processing line... 920s /usr/bin/bowtie2 --local --trim5 0 --score-min L,5.19834192928815,8.28188684534299 --np 1 --cp-min 2 --cp-ival 1 -r -p 2 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s Processing line... 920s --- Summary --- 920s Read 1 reference strings 920s Checked 0 alignments, 0 edits 920s --------------- 920s PASSED 920s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 920s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 920s Warning: skipping mate #1 of read '34' because it was < 2 characters long 920s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 920s Warning: skipping mate #2 of read '40' because it was < 2 characters long 920s 77 reads; of these: 920s 77 (100.00%) were paired; of these: 920s 77 (100.00%) aligned concordantly 0 times 920s 0 (0.00%) aligned concordantly exactly 1 time 920s 0 (0.00%) aligned concordantly >1 times 920s ---- 920s 77 pairs aligned concordantly 0 times; of these: 920s 0 (0.00%) aligned discordantly 1 time 920s ---- 920s 77 pairs aligned 0 times concordantly or discordantly; of these: 920s 154 mates make up the pairs; of these: 920s 154 (100.00%) aligned 0 times 920s 0 (0.00%) aligned exactly 1 time 920s 0 (0.00%) aligned >1 times 920s 0.00% overall alignment rate 920s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 920s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 920s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 920s Flattened IUPAC characters 920s Mutating sequence Sim.pm.2 920s Introducing 15 SNPs, 3/0 ref/read gaps, and 1 rearrangements 920s Finished SNPs 920s Finished ref gaps 920s Finished read gaps 920s Mutating sequence Sim.pm.1 920s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 920s Finished SNPs 920s Finished ref gaps 920s Finished read gaps 920s Mutated reference genome to subject genome 920s SNPs introduced: 17 920s Reference gaps introduced: 3 920s Read gaps introduced: 0 920s Rearrangements introduced: 1 920s Created read sampler 920s Sampling 172 reads 920s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 920s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 920s parsing sequence Sim.pm.1... 920s parsing sequence Sim.pm.2... 920s *** Run 70 of 100 920s /usr/bin/bowtie2 --cp-ival 3 --cp-min 3 --gbar 3 --score-min L,1.40461277141799,7.22904682181263 --rfg 5.89964798906356,6.46428532035288 --local --mp 7.86010316205619,7.37643297668398 -a -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 920s Parsed 74 reference bases 921s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 921s Warning: skipping read '4' because it was < 2 characters long 921s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 921s Warning: skipping read '44' because it was < 2 characters long 921s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 921s Warning: skipping read '64' because it was < 2 characters long 921s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 921s Warning: skipping read '81' because it was < 2 characters long 921s Warning: skipping read '84' because length (1) <= # seed mismatches (0) 921s Warning: skipping read '84' because it was < 2 characters long 921s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 921s Warning: skipping read '99' because it was < 2 characters long 921s Warning: skipping read '114' because length (1) <= # seed mismatches (0) 921s Warning: skipping read '114' because it was < 2 characters long 921s Warning: skipping read '150' because length (1) <= # seed mismatches (0) 921s Read 50 alignments... 921s Read 100 alignments... 921s Warning: skipping read '150' because it was < 2 characters long 921s Warning: skipping read '152' because length (1) <= # seed mismatches (0) 921s Warning: skipping read '152' because it was < 2 characters long 921s Warning: skipping read '168' because length (1) <= # seed mismatches (0) 921s Warning: skipping read '168' because it was < 2 characters long 921s 172 reads; of these: 921s 172 (100.00%) were unpaired; of these: 921s 172 (100.00%) aligned 0 times 921s 0 (0.00%) aligned exactly 1 time 921s 0 (0.00%) aligned >1 times 921s 0.00% overall alignment rate 921s Read 150 alignments... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s --- Summary --- 921s Read 1 reference strings 921s Checked 0 alignments, 0 edits 921s --------------- 921s PASSED 921s Flattened IUPAC characters 921s Mutating sequence Sim.pm.1 921s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 921s Finished SNPs 921s Finished ref gaps 921s Finished read gaps 921s Mutating sequence Sim.pm.2 921s Introducing 11 SNPs, 1/0 ref/read gaps, and 0 rearrangements 921s Finished SNPs 921s Finished ref gaps 921s Finished read gaps 921s Mutated reference genome to subject genome 921s *** Run 71 of 100 921s /usr/bin/bowtie2 --cp-min 15 --nofw --cp-ival 2 --trim5 2 --rdg 24.132496837183,1.50264304770374 --rfg 46.1717322397033 --ma 25.6064371445902 --score-min L,9.45305697923053,4.47326986781691 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 921s SNPs introduced: 14 921s Reference gaps introduced: 1 921s Read gaps introduced: 0 921s Rearrangements introduced: 0 921s Created read sampler 921s Sampling 104 reads 921s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 921s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 921s parsing sequence Sim.pm.1... 921s parsing sequence Sim.pm.2... 921s Parsed 74 reference bases 921s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 921s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 921s Warning: skipping mate #2 of read '8' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 921s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 921s Warning: skipping mate #1 of read '17' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 921s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 921s Warning: skipping mate #2 of read '24' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 921s Read 50 alignments... 921s Read 100 alignments... 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 921s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 921s Warning: skipping mate #1 of read '75' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 921s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 921s Warning: skipping mate #1 of read '88' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 921s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 921s Warning: skipping mate #1 of read '89' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 921s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 921s Warning: skipping mate #2 of read '90' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 921s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (0) 921s Warning: skipping mate #2 of read '94' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 921s 104 reads; of these: 921s 98 (94.23%) were paired; of these: 921s 98 (100.00%) aligned concordantly 0 times 921s 0 (0.00%) aligned concordantly exactly 1 time 921s 0 (0.00%) aligned concordantly >1 times 921s ---- 921s 98 pairs aligned concordantly 0 times; of these: 921s 0 (0.00%) aligned discordantly 1 time 921s ---- 921s 98 pairs aligned 0 times concordantly or discordantly; of these: 921s 196 mates make up the pairs; of these: 921s 174 (88.78%) aligned 0 times 921s 12 (6.12%) aligned exactly 1 time 921s 10 (5.10%) aligned >1 times 921s 6 (5.77%) were unpaired; of these: 921s 4 (66.67%) aligned 0 times 921s 2 (33.33%) aligned exactly 1 time 921s 0 (0.00%) aligned >1 times 921s 11.88% overall alignment rate 921s Read 150 alignments... 921s Read 200 alignments... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s GC 921s GC 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s GGTAA 921s GGTAA 921s Processing line... 921s Processing line... 921s TCTTTACACAAAGAGGC 921s TCTTTACACAAAGAGGC 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s CTTTACACAA 921s CTTTACACAA 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s CT 921s CT 921s Processing line... 921s Processing line... 921s ACAAA 921s ACAAA 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s TTA 921s TTA 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s GGGTGTACATG 921s GGGTGTACATG 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s TGA 921s TGA 921s Processing line... 921s Processing line... 921s TCTTTACACAAAGAGGC 921s TCTTTACACAAAGAGGC 921s Processing line... 921s Processing line... 921s GGGT 921s GGGT 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s CTT 921s CTT 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s GA 921s GA 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s TG 921s TG 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s AAAGA 921s AAAGA 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s AT 921s AT 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s CATGACTCTTTACACAAAG 921s CATGACTCTTTACACAAAG 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s GC 921s GC 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s AC 921s AC 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s AGCT 921s AGCT 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s GGTG 921s GGTG 921s Processing line... 921s Processing line... 921s AC 921s AC 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s AAGAGGCG 921s AAGAGGCG 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s Processing line... 921s CT 921s CT 921s Processing line... 921s --- Summary --- 921s Read 1 reference strings 921s Checked 24 alignments, 0 edits 921s --------------- 921s PASSED 921s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 921s /usr/bin/bowtie2 --cp-min 15 --nofw --cp-ival 2 --trim5 2 --rdg 24.132496837183,1.50264304770374 --rfg 46.1717322397033 --ma 25.6064371445902 --score-min L,9.45305697923053,4.47326986781691 -q -p 3 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 921s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 921s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 921s Warning: skipping mate #2 of read '8' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 921s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 921s Warning: skipping mate #1 of read '17' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 921s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 921s Warning: skipping mate #2 of read '24' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 921s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 921s Warning: skipping mate #1 of read '88' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 921s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 921s Warning: skipping mate #1 of read '89' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 921s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 921s Warning: skipping mate #2 of read '90' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 921s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (0) 921s Warning: skipping mate #2 of read '94' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 921s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 921s Warning: skipping mate #1 of read '75' because it was < 2 characters long 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 921s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 921s 104 reads; of these: 921s 98 (94.23%) were paired; of these: 921s 98 (100.00%) aligned concordantly 0 times 921s 0 (0.00%) aligned concordantly exactly 1 time 921s 0 (0.00%) aligned concordantly >1 times 921s ---- 921s 98 pairs aligned concordantly 0 times; of these: 921s 0 (0.00%) aligned discordantly 1 time 921s ---- 921s 98 pairs aligned 0 times concordantly or discordantly; of these: 921s 196 mates make up the pairs; of these: 921s 174 (88.78%) aligned 0 times 921s 12 (6.12%) aligned exactly 1 time 921s 10 (5.10%) aligned >1 times 921s 6 (5.77%) were unpaired; of these: 921s 4 (66.67%) aligned 0 times 921s 2 (33.33%) aligned exactly 1 time 921s 0 (0.00%) aligned >1 times 921s 11.88% overall alignment rate 921s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 921s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 921s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 921s Flattened IUPAC characters 921s Mutating sequence Sim.pm.2 921s Introducing 16 SNPs, 6/0 ref/read gaps, and 1 rearrangements 921s Finished SNPs 921s Finished ref gaps 921s Finished read gaps 921s Mutating sequence Sim.pm.1 921s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 921s Finished SNPs 921s Finished ref gaps 921s Finished read gaps 921s Mutated reference genome to subject genome 921s SNPs introduced: 19 921s Reference gaps introduced: 6 921s Read gaps introduced: 0 921s Rearrangements introduced: 2 921s Created read sampler 921s Sampling 83 reads 921s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 921s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 921s parsing sequence Sim.pm.1... 921s parsing sequence Sim.pm.2... 921s Parsed 74 reference bases 921s *** Run 72 of 100 921s /usr/bin/bowtie2 -k 2 --trim3 3 --mp 5.62058098462847,3.62397850772281 --cp-ival 1 --cp-min 4 --n-ceil 1.1296088823661,0.495542684393529 --score-min L,7.10039913725757,9.53523508482379 --trim5 2 --rfg 41.3383930184708 -N 1 -L23 -R 2 -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 922s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 922s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '4' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 922s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '10' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 922s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '12' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 922s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '14' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 922s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '15' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 922s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '20' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 922s Warning: skipping read '36' because length (1) <= # seed mismatches (1) 922s Warning: skipping read '36' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 922s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '38' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 922s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '41' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 922s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '45' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 922s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '54' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 922s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '67' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 922s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '70' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 922s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '73' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 922s Warning: skipping read '74' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '74' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 922s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '77' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 922s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '82' because it was < 2 characters long 922s 83 reads; of these: 922s 83 (100.00%) were unpaired; of these: 922s 76 (91.57%) aligned 0 times 922s 4 (4.82%) aligned exactly 1 time 922s 3 (3.61%) aligned >1 times 922s 8.43% overall alignment rate 922s Read 50 alignments... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s CTCTTTACACAAAGAGGCGG 922s CTCTTTACACAAAGAGGCGG 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s AT 922s AT 922s Processing line... 922s AT 922s AT 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s AAAGAGGCGG 922s AAAGAGGCGG 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s CAG 922s CAG 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s AGAGGC 922s AGAGGC 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s AGG 922s AGG 922s Processing line... 922s AGG 922s AGG 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s GAGG 922s GAGG 922s Processing line... 922s GAGG 922s GAGG 922s Processing line... 922s Processing line... 922s Processing line... 922s --- Summary --- 922s Read 1 reference strings 922s Checked 10 alignments, 0 edits 922s --------------- 922s PASSED 922s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 922s /usr/bin/bowtie2 -k 2 --trim3 3 --mp 5.62058098462847,3.62397850772281 --cp-ival 1 --cp-min 4 --n-ceil 1.1296088823661,0.495542684393529 --score-min L,7.10039913725757,9.53523508482379 --trim5 2 --rfg 41.3383930184708 -N 1 -L23 -R 2 -r -p 4 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 922s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 922s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '20' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 922s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '4' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 922s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '10' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 922s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '12' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 922s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '14' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 922s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '15' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 922s Warning: skipping read '36' because length (1) <= # seed mismatches (1) 922s Warning: skipping read '36' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 922s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '38' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 922s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '41' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 922s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '45' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 922s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '67' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 922s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '70' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 922s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '73' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 922s Warning: skipping read '74' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '74' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 922s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '77' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 922s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '82' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 922s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 922s Warning: skipping read '54' because it was < 2 characters long 922s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 922s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 922s 83 reads; of these: 922s 83 (100.00%) were unpaired; of these: 922s 76 (91.57%) aligned 0 times 922s 4 (4.82%) aligned exactly 1 time 922s 3 (3.61%) aligned >1 times 922s 8.43% overall alignment rate 922s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 922s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 922s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 922s *** Run 73 of 100 922s /usr/bin/bowtie2 --cp-ival 1 -R 2 --mm --cp-min 2 --np 25 -k 3 --score-min L,9.93630780539763,6.64986959855953 --trim3 0 --trim5 4 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq 922s Flattened IUPAC characters 922s Mutating sequence Sim.pm.1 922s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 922s Finished SNPs 922s Finished ref gaps 922s Finished read gaps 922s Mutating sequence Sim.pm.2 922s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 922s Finished SNPs 922s Finished ref gaps 922s Finished read gaps 922s Mutated reference genome to subject genome 922s SNPs introduced: 9 922s Reference gaps introduced: 0 922s Read gaps introduced: 0 922s Rearrangements introduced: 1 922s Created read sampler 922s Sampling 30 reads 922s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 922s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 922s parsing sequence Sim.pm.1... 922s parsing sequence Sim.pm.2... 922s Parsed 74 reference bases 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 922s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 922s 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 922s 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 922s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 922s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 922s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 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 922s 30 reads; of these: 922s 28 (93.33%) were paired; of these: 922s 27 (96.43%) aligned concordantly 0 times 922s 1 (3.57%) aligned concordantly exactly 1 time 922s 0 (0.00%) aligned concordantly >1 times 922s ---- 922s 27 pairs aligned concordantly 0 times; of these: 922s 1 (3.70%) aligned discordantly 1 time 922s ---- 922s 26 pairs aligned 0 times concordantly or discordantly; of these: 922s 52 mates make up the pairs; of these: 922s 41 (78.85%) aligned 0 times 922s 8 (15.38%) aligned exactly 1 time 922s 3 (5.77%) aligned >1 times 922s 2 (6.67%) were unpaired; of these: 922s 2 (100.00%) aligned 0 times 922s 0 (0.00%) aligned exactly 1 time 922s 0 (0.00%) aligned >1 times 922s 25.86% overall alignment rate 922s /usr/bin/bowtie2 --cp-ival 1 -R 2 --mm --cp-min 2 --np 25 -k 3 --score-min L,9.93630780539763,6.64986959855953 --trim3 0 --trim5 4 --qseq -p 4 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 922s Read 50 alignments... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s CG 922s CG 922s Processing line... 922s CG 922s CG 922s Processing line... 922s CG 922s CG 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s GGGCGATAAGGGC 922s GGGCGATAAGGGC 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s GGGTAACATTC 922s GGGTAACATTC 922s Processing line... 922s Processing line... 922s GACTCTTTACACAAAGAG 922s GACTCTTTACACAAAGAG 922s Processing line... 922s Processing line... 922s CAAAGAGGCG 922s CAAAGAGGCG 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s CGGGGTAACAT 922s CGGGGTAACAT 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s AAGAGGCGGGGTAACAT 922s AAGAGGCGGGGTAACAT 922s Processing line... 922s GGGTAACATT 922s GGGTAACATT 922s Processing line... 922s GGGTAACATTC 922s GGGTAACATTC 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s AGG 922s AGG 922s Processing line... 922s AGG 922s AGG 922s Processing line... 922s AGG 922s AGG 922s Processing line... 922s Processing line... 922s TTACACAAAGAGGCGGGGTAACATTCAG 922s TTACACAAAGAGGCGGGGTAACATTCAG 922s Processing line... 922s Processing line... 922s CGAT 922s CGAT 922s Processing line... 922s AGAGGCGGGGT 922s AGAGGCGGGGT 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s Processing line... 922s GGT 922s GGT 922s Processing line... 922s ACC 922s ACC 922s Processing line... 922s GGT 922s GGT 922s Processing line... 922s Processing line... 922s TGTACATGACTCTTTACAC 922s TGTACATGACTCTTTACAC 922s Processing line... 922s --- Summary --- 922s Read 1 reference strings 922s Checked 21 alignments, 0 edits 922s --------------- 922s PASSED 922s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 923s 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 923s 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 923s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 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 923s 30 reads; of these: 923s 28 (93.33%) were paired; of these: 923s 27 (96.43%) aligned concordantly 0 times 923s 1 (3.57%) aligned concordantly exactly 1 time 923s 0 (0.00%) aligned concordantly >1 times 923s ---- 923s 27 pairs aligned concordantly 0 times; of these: 923s 1 (3.70%) aligned discordantly 1 time 923s ---- 923s 26 pairs aligned 0 times concordantly or discordantly; of these: 923s 52 mates make up the pairs; of these: 923s 41 (78.85%) aligned 0 times 923s 8 (15.38%) aligned exactly 1 time 923s 3 (5.77%) aligned >1 times 923s 2 (6.67%) were unpaired; of these: 923s 2 (100.00%) aligned 0 times 923s 0 (0.00%) aligned exactly 1 time 923s 0 (0.00%) aligned >1 times 923s 25.86% overall alignment rate 923s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 923s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 923s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 923s Flattened IUPAC characters 923s Mutating sequence Sim.pm.2 923s Introducing 2 SNPs, 2/2 ref/read gaps, and 0 rearrangements 923s Finished SNPs 923s Finished ref gaps 923s Finished read gaps 923s Mutating sequence Sim.pm.1 923s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 923s Finished SNPs 923s Finished ref gaps 923s Finished read gaps 923s Mutated reference genome to subject genome 923s SNPs introduced: 9 923s Reference gaps introduced: 2 923s Read gaps introduced: 2 923s Rearrangements introduced: 1 923s Created read sampler 923s Sampling 46 reads 923s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 923s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 923s parsing sequence Sim.pm.1... 923s parsing sequence Sim.pm.2... 923s Parsed 74 reference bases 923s *** Run 74 of 100 923s /usr/bin/bowtie2 --np 2 --nofw --gbar 5 --score-min L,7.53915587339003,7.01792501636018 --rfg 2.17342007008414 --trim5 5 --cp-ival 1 --cp-min 3 --local --trim3 5 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 923s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '2' because it was < 2 characters long 923s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #2 of read '4' because it was < 2 characters long 923s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '5' because it was < 2 characters long 923s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '12' because it was < 2 characters long 923s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '15' because it was < 2 characters long 923s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '17' because it was < 2 characters long 923s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 923s Warning: skipping read '18' because it was < 2 characters long 923s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '21' because it was < 2 characters long 923s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '22' because it was < 2 characters long 923s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '23' because it was < 2 characters long 923s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 923s Warning: skipping read '24' because it was < 2 characters long 923s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '25' because it was < 2 characters long 923s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '26' because it was < 2 characters long 923s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '28' because it was < 2 characters long 923s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '30' because it was < 2 characters long 923s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '34' because it was < 2 characters long 923s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '37' because it was < 2 characters long 923s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '40' because it was < 2 characters long 923s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '43' because it was < 2 characters long 923s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '44' because it was < 2 characters long 923s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #2 of read '45' because it was < 2 characters long 923s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '46' because it was < 2 characters long 923s 46 reads; of these: 923s 39 (84.78%) were paired; of these: 923s 39 (100.00%) aligned concordantly 0 times 923s 0 (0.00%) aligned concordantly exactly 1 time 923s 0 (0.00%) aligned concordantly >1 times 923s ---- 923s 39 pairs aligned concordantly 0 times; of these: 923s 0 (0.00%) aligned discordantly 1 time 923s ---- 923s 39 pairs aligned 0 times concordantly or discordantly; of these: 923s 78 mates make up the pairs; of these: 923s 78 (100.00%) aligned 0 times 923s 0 (0.00%) aligned exactly 1 time 923s 0 (0.00%) aligned >1 times 923s 7 (15.22%) were unpaired; of these: 923s 7 (100.00%) aligned 0 times 923s 0 (0.00%) aligned exactly 1 time 923s 0 (0.00%) aligned >1 times 923s 0.00% overall alignment rate 923s Read 50 alignments... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s Processing line... 923s --- Summary --- 923s Read 1 reference strings 923s Checked 0 alignments, 0 edits 923s --------------- 923s PASSED 923s ALSO checking that bowtie2 and bowtie2-align match up 923s /usr/bin/bowtie2 --np 2 --nofw --gbar 5 --score-min L,7.53915587339003,7.01792501636018 --rfg 2.17342007008414 --trim5 5 --cp-ival 1 --cp-min 3 --local --trim3 5 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 923s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '2' because it was < 2 characters long 923s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #2 of read '4' because it was < 2 characters long 923s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '5' because it was < 2 characters long 923s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '12' because it was < 2 characters long 923s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '15' because it was < 2 characters long 923s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '17' because it was < 2 characters long 923s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 923s Warning: skipping read '18' because it was < 2 characters long 923s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '21' because it was < 2 characters long 923s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '22' because it was < 2 characters long 923s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '23' because it was < 2 characters long 923s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 923s Warning: skipping read '24' because it was < 2 characters long 923s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '25' because it was < 2 characters long 923s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '26' because it was < 2 characters long 923s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '28' because it was < 2 characters long 923s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '30' because it was < 2 characters long 923s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '34' because it was < 2 characters long 923s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '37' because it was < 2 characters long 923s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '40' because it was < 2 characters long 923s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '43' because it was < 2 characters long 923s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '44' because it was < 2 characters long 923s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #2 of read '45' because it was < 2 characters long 923s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '46' because it was < 2 characters long 923s 46 reads; of these: 923s 39 (84.78%) were paired; of these: 923s 39 (100.00%) aligned concordantly 0 times 923s 0 (0.00%) aligned concordantly exactly 1 time 923s 0 (0.00%) aligned concordantly >1 times 923s ---- 923s 39 pairs aligned concordantly 0 times; of these: 923s 0 (0.00%) aligned discordantly 1 time 923s ---- 923s 39 pairs aligned 0 times concordantly or discordantly; of these: 923s 78 mates make up the pairs; of these: 923s 78 (100.00%) aligned 0 times 923s 0 (0.00%) aligned exactly 1 time 923s 0 (0.00%) aligned >1 times 923s 7 (15.22%) were unpaired; of these: 923s 7 (100.00%) aligned 0 times 923s 0 (0.00%) aligned exactly 1 time 923s 0 (0.00%) aligned >1 times 923s 0.00% overall alignment rate 923s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 923s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 923s /usr/bin/bowtie2 --np 2 --nofw --gbar 5 --score-min L,7.53915587339003,7.01792501636018 --rfg 2.17342007008414 --trim5 5 --cp-ival 1 --cp-min 3 --local --trim3 5 -f -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 923s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '2' because it was < 2 characters long 923s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #2 of read '4' because it was < 2 characters long 923s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '5' because it was < 2 characters long 923s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '12' because it was < 2 characters long 923s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '15' because it was < 2 characters long 923s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '17' because it was < 2 characters long 923s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 923s Warning: skipping read '18' because it was < 2 characters long 923s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '21' because it was < 2 characters long 923s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '22' because it was < 2 characters long 923s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '23' because it was < 2 characters long 923s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 923s Warning: skipping read '24' because it was < 2 characters long 923s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '25' because it was < 2 characters long 923s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '26' because it was < 2 characters long 923s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '28' because it was < 2 characters long 923s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '30' because it was < 2 characters long 923s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '34' because it was < 2 characters long 923s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '37' because it was < 2 characters long 923s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '40' because it was < 2 characters long 923s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '43' because it was < 2 characters long 923s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '44' because it was < 2 characters long 923s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 923s Warning: skipping mate #2 of read '45' because it was < 2 characters long 923s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 923s Warning: skipping mate #1 of read '46' because it was < 2 characters long 923s 46 reads; of these: 923s 39 (84.78%) were paired; of these: 923s 39 (100.00%) aligned concordantly 0 times 923s 0 (0.00%) aligned concordantly exactly 1 time 923s 0 (0.00%) aligned concordantly >1 times 923s ---- 923s 39 pairs aligned concordantly 0 times; of these: 923s 0 (0.00%) aligned discordantly 1 time 923s ---- 923s 39 pairs aligned 0 times concordantly or discordantly; of these: 923s 78 mates make up the pairs; of these: 923s 78 (100.00%) aligned 0 times 923s 0 (0.00%) aligned exactly 1 time 923s 0 (0.00%) aligned >1 times 923s 7 (15.22%) were unpaired; of these: 923s 7 (100.00%) aligned 0 times 923s 0 (0.00%) aligned exactly 1 time 923s 0 (0.00%) aligned >1 times 923s 0.00% overall alignment rate 923s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 923s Flattened IUPAC characters 923s *** Run 75 of 100 923s /usr/bin/bowtie2 --mp 8.28472429569884,6.88645455816232 --rdg 1.41832278462007 --trim5 5 --score-min L,7.22799297346706,8.53723193829168 --n-ceil 1.46220345319588,0.414977110350996 --cp-min 3 --cp-ival 1 --mm -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 923s Mutating sequence Sim.pm.2 923s Introducing 9 SNPs, 2/0 ref/read gaps, and 0 rearrangements 923s Finished SNPs 923s Finished ref gaps 923s Finished read gaps 923s Mutating sequence Sim.pm.1 923s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 923s Finished SNPs 923s Finished ref gaps 923s Finished read gaps 923s Mutated reference genome to subject genome 923s SNPs introduced: 11 923s Reference gaps introduced: 2 923s Read gaps introduced: 0 923s Rearrangements introduced: 0 923s Created read sampler 923s Sampling 69 reads 923s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 923s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 923s parsing sequence Sim.pm.1... 923s parsing sequence Sim.pm.2... 923s Parsed 74 reference bases 924s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 924s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '8' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 924s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '9' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 924s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '11' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 924s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '17' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 924s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '18' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 924s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '37' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 924s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '38' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 924s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '41' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 924s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '42' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 924s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '50' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 924s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '52' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 924s 69 reads; of these: 924s 69 (100.00%) were unpaired; of these: 924s 58 (84.06%) aligned 0 times 924s 4 (5.80%) aligned exactly 1 time 924s 7 (10.14%) aligned >1 times 924s 15.94% overall alignment rate 924s Read 50 alignments... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s AAGAGG 924s AAGAGG 924s Processing line... 924s Processing line... 924s Processing line... 924s GAGG 924s GAGG 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s GGGCG 924s GGGCG 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s TA 924s TA 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s CG 924s CG 924s Processing line... 924s Processing line... 924s Processing line... 924s CATG 924s CATG 924s Processing line... 924s Processing line... 924s AACAT 924s AACAT 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s /usr/bin/bowtie2 --mp 8.28472429569884,6.88645455816232 --rdg 1.41832278462007 --trim5 5 --score-min L,7.22799297346706,8.53723193829168 --n-ceil 1.46220345319588,0.414977110350996 --cp-min 3 --cp-ival 1 --mm -f -p 4 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s AAGAGGC 924s AAGAGGC 924s Processing line... 924s Processing line... 924s GC 924s GC 924s Processing line... 924s Processing line... 924s AAA 924s AAA 924s Processing line... 924s GCGGGGTAACATTCAGCTA 924s GCGGGGTAACATTCAGCTA 924s Processing line... 924s Processing line... 924s Processing line... 924s --- Summary --- 924s Read 1 reference strings 924s Checked 11 alignments, 0 edits 924s --------------- 924s PASSED 924s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 924s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 924s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '8' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 924s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '9' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 924s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '11' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 924s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '17' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 924s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '18' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 924s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '50' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 924s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '52' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 924s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '37' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 924s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '38' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 924s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '41' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 924s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '42' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 924s 69 reads; of these: 924s 69 (100.00%) were unpaired; of these: 924s 58 (84.06%) aligned 0 times 924s 4 (5.80%) aligned exactly 1 time 924s 7 (10.14%) aligned >1 times 924s 15.94% overall alignment rate 924s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 924s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 924s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 924s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 924s /usr/bin/bowtie2 --mp 8.28472429569884,6.88645455816232 --rdg 1.41832278462007 --trim5 5 --score-min L,7.22799297346706,8.53723193829168 --n-ceil 1.46220345319588,0.414977110350996 --cp-min 3 --cp-ival 1 --mm -f -p 3 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 924s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 924s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '8' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 924s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '9' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 924s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '11' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 924s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '17' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 924s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '18' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 924s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '50' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 924s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '52' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 924s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '37' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 924s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '38' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 924s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '41' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 924s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 924s Warning: skipping read '42' because it was < 2 characters long 924s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 924s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 924s 69 reads; of these: 924s 69 (100.00%) were unpaired; of these: 924s 58 (84.06%) aligned 0 times 924s 4 (5.80%) aligned exactly 1 time 924s 7 (10.14%) aligned >1 times 924s 15.94% overall alignment rate 924s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 924s Flattened IUPAC characters 924s Mutating sequence Sim.pm.1 924s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 924s Finished SNPs 924s Finished ref gaps 924s Finished read gaps 924s Mutating sequence Sim.pm.2 924s Introducing 9 SNPs, 1/1 ref/read gaps, and 1 rearrangements 924s Finished SNPs 924s Finished ref gaps 924s Finished read gaps 924s Mutated reference genome to subject genome 924s SNPs introduced: 10 924s Reference gaps introduced: 1 924s Read gaps introduced: 1 924s Rearrangements introduced: 1 924s Created read sampler 924s Sampling 100 reads 924s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 924s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 924s *** Run 76 of 100 924s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --local -a --mp 6.43693868496446,5.68952913983258 --trim3 3 -D 29 -N 0 -L29 --nofw --score-min L,5.39820791541025,5.39729013888615 --trim5 9 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq 924s parsing sequence Sim.pm.1... 924s parsing sequence Sim.pm.2... 924s Parsed 74 reference bases 924s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 924s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 924s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 924s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 924s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 924s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 924s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 924s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 924s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 924s Read 50 alignments... 924s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 924s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 924s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 924s Read 100 alignments... 924s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 924s Warning: skipping read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 924s Warning: skipping read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 924s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (1) <= # seed mismatches (0) 924s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 924s 100 reads; of these: 924s 72 (72.00%) were paired; of these: 924s 72 (100.00%) aligned concordantly 0 times 924s 0 (0.00%) aligned concordantly exactly 1 time 924s 0 (0.00%) aligned concordantly >1 times 924s ---- 924s 72 pairs aligned concordantly 0 times; of these: 924s 0 (0.00%) aligned discordantly 1 time 924s ---- 924s 72 pairs aligned 0 times concordantly or discordantly; of these: 924s 144 mates make up the pairs; of these: 924s 144 (100.00%) aligned 0 times 924s 0 (0.00%) aligned exactly 1 time 924s 0 (0.00%) aligned >1 times 924s 28 (28.00%) were unpaired; of these: 924s 28 (100.00%) aligned 0 times 924s 0 (0.00%) aligned exactly 1 time 924s 0 (0.00%) aligned >1 times 924s 0.00% overall alignment rate 924s Read 150 alignments... 924s Processing line... 924s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --local -a --mp 6.43693868496446,5.68952913983258 --trim3 3 -D 29 -N 0 -L29 --nofw --score-min L,5.39820791541025,5.39729013888615 --trim5 9 --qseq -p 2 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s Processing line... 924s --- Summary --- 924s Read 1 reference strings 924s Checked 0 alignments, 0 edits 924s --------------- 924s PASSED 924s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 925s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 925s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 925s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 925s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 925s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 925s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 925s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 925s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 925s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 925s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 925s Warning: skipping read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (1) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 925s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 925s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 925s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 925s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 925s 100 reads; of these: 925s 72 (72.00%) were paired; of these: 925s 72 (100.00%) aligned concordantly 0 times 925s 0 (0.00%) aligned concordantly exactly 1 time 925s 0 (0.00%) aligned concordantly >1 times 925s ---- 925s 72 pairs aligned concordantly 0 times; of these: 925s 0 (0.00%) aligned discordantly 1 time 925s ---- 925s 72 pairs aligned 0 times concordantly or discordantly; of these: 925s 144 mates make up the pairs; of these: 925s 144 (100.00%) aligned 0 times 925s 0 (0.00%) aligned exactly 1 time 925s 0 (0.00%) aligned >1 times 925s 28 (28.00%) were unpaired; of these: 925s 28 (100.00%) aligned 0 times 925s 0 (0.00%) aligned exactly 1 time 925s 0 (0.00%) aligned >1 times 925s 0.00% overall alignment rate 925s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 925s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 925s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 925s Flattened IUPAC characters 925s Mutating sequence Sim.pm.2 925s Introducing 4 SNPs, 0/3 ref/read gaps, and 0 rearrangements 925s Finished SNPs 925s Finished ref gaps 925s Finished read gaps 925s Mutating sequence Sim.pm.1 925s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 925s Finished SNPs 925s Finished ref gaps 925s Finished read gaps 925s Mutated reference genome to subject genome 925s SNPs introduced: 7 925s Reference gaps introduced: 1 925s Read gaps introduced: 3 925s Rearrangements introduced: 1 925s Created read sampler 925s Sampling 123 reads 925s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 925s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 925s parsing sequence Sim.pm.1... 925s *** Run 77 of 100 925s /usr/bin/bowtie2 --cp-min 2 --cp-ival 2 --trim3 1 --norc --nofw --np 1 -N 0 -L27 --trim5 1 --score-min L,9.63307175962771,1.10975625288174 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 925s parsing sequence Sim.pm.2... 925s Parsed 74 reference bases 925s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 925s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '3' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 925s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '41' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 925s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '46' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 925s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '50' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 925s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '60' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 925s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '62' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 925s Warning: skipping read '73' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '73' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 925s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '76' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 925s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '87' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 925s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '114' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 925s 123 reads; of these: 925s 123 (100.00%) were unpaired; of these: 925s 123 (100.00%) aligned 0 times 925s 0 (0.00%) aligned exactly 1 time 925s 0 (0.00%) aligned >1 times 925s 0.00% overall alignment rate 925s Read 50 alignments... 925s Read 100 alignments... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s Processing line... 925s --- Summary --- 925s Read 1 reference strings 925s Checked 0 alignments, 0 edits 925s --------------- 925s PASSED 925s ALSO checking that bowtie2 and bowtie2-align match up 925s /usr/bin/bowtie2 --cp-min 2 --cp-ival 2 --trim3 1 --norc --nofw --np 1 -N 0 -L27 --trim5 1 --score-min L,9.63307175962771,1.10975625288174 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 925s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 925s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '3' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 925s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '41' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 925s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '46' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 925s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '50' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 925s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '60' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 925s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '62' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 925s Warning: skipping read '73' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '73' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 925s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '76' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 925s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '87' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 925s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '114' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 925s 123 reads; of these: 925s 123 (100.00%) were unpaired; of these: 925s 123 (100.00%) aligned 0 times 925s 0 (0.00%) aligned exactly 1 time 925s 0 (0.00%) aligned >1 times 925s 0.00% overall alignment rate 925s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 925s /usr/bin/bowtie2 --cp-min 2 --cp-ival 2 --trim3 1 --norc --nofw --np 1 -N 0 -L27 --trim5 1 --score-min L,9.63307175962771,1.10975625288174 -q -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 925s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 925s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 925s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '3' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 925s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '41' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 925s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '46' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 925s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '50' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 925s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '60' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 925s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '62' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 925s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '87' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 925s Warning: skipping read '73' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '73' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 925s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 925s Warning: skipping read '76' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 925s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 925s Warning: skipping read '114' because it was < 2 characters long 925s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 925s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 925s 123 reads; of these: 925s 123 (100.00%) were unpaired; of these: 925s 123 (100.00%) aligned 0 times 925s 0 (0.00%) aligned exactly 1 time 925s 0 (0.00%) aligned >1 times 925s 0.00% overall alignment rate 925s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 925s Flattened IUPAC characters 925s Mutating sequence Sim.pm.1 925s Introducing 1 SNPs, 1/1 ref/read gaps, and 1 rearrangements 925s Finished SNPs 925s Finished ref gaps 925s Finished read gaps 925s Mutating sequence Sim.pm.2 925s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 925s Finished SNPs 925s Finished ref gaps 925s Finished read gaps 925s Mutated reference genome to subject genome 925s SNPs introduced: 1 925s Reference gaps introduced: 1 925s Read gaps introduced: 2 925s Rearrangements introduced: 1 925s Created read sampler 925s Sampling 76 reads 925s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 925s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 925s parsing sequence Sim.pm.1... 925s *** Run 78 of 100 925s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 4 --np 1 --ma 27.1514831040409 -k 2 --score-min L,4.07813647186458,6.11993860648702 --trim5 2 -i S -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 925s parsing sequence Sim.pm.2... 925s Parsed 74 reference bases 926s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 926s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read '3' because it was < 2 characters long 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 926s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read '10' because it was < 2 characters long 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 926s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read '12' because it was < 2 characters long 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 926s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read '34' because it was < 2 characters long 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 926s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read '35' because it was < 2 characters long 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 926s Read 50 alignments... 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 926s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read '53' because it was < 2 characters long 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 926s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 926s 76 reads; of these: 926s 74 (97.37%) were paired; of these: 926s 73 (98.65%) aligned concordantly 0 times 926s 0 (0.00%) aligned concordantly exactly 1 time 926s 1 (1.35%) aligned concordantly >1 times 926s ---- 926s 73 pairs aligned concordantly 0 times; of these: 926s 3 (4.11%) aligned discordantly 1 time 926s ---- 926s 70 pairs aligned 0 times concordantly or discordantly; of these: 926s 140 mates make up the pairs; of these: 926s 115 (82.14%) aligned 0 times 926s 21 (15.00%) aligned exactly 1 time 926s 4 (2.86%) aligned >1 times 926s 2 (2.63%) were unpaired; of these: 926s 2 (100.00%) aligned 0 times 926s 0 (0.00%) aligned exactly 1 time 926s 0 (0.00%) aligned >1 times 926s 22.00% overall alignment rate 926s Read 100 alignments... 926s Read 150 alignments... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s GTAAC 926s GTAAC 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s CATTCAG 926s CATTCAG 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s CACAA 926s CACAA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s ACA 926s ACA 926s Processing line... 926s GGGTAACATTCAGC 926s GGGTAACATTCAGC 926s Processing line... 926s ACA 926s ACA 926s Processing line... 926s GGGTAACATTCAGC 926s GGGTAACATTCAGC 926s Processing line... 926s Processing line... 926s Processing line... 926s GACTCTTTAC 926s GACTCTTTAC 926s Processing line... 926s TT 926s TT 926s Processing line... 926s TT 926s TT 926s Processing line... 926s CATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCTA 926s CATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCTA 926s Processing line... 926s Processing line... 926s GGGGTAACATTCAG 926s GGGGTAACATTCAG 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s ACAAAGAGGCGGGGT 926s ACAAAGAGGCGGGGT 926s Processing line... 926s Processing line... 926s GAG 926s GAG 926s Processing line... 926s GAG 926s GAG 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s GTACATGACTCTTTACACAAAGAGGCGGGGTAA 926s GTACATGACTCTTTACACAAAGAGGCGGGGTAA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s GGGTAAC 926s GGGTAAC 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s ATGACTCTTTACACAAA 926s ATGACTCTTTACACAAA 926s Processing line... 926s Processing line... 926s CTTTACACAAA 926s CTTTACACAAA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s TTCA 926s TTCA 926s Processing line... 926s GGTGTACATGACTCTT 926s GGTGTACATGACTCTT 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s AGAGGCGGGG 926s AGAGGCGGGG 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s CAA 926s CAA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s CTCTTT 926s CTCTTT 926s Processing line... 926s AAAGAG 926s AAAGAG 926s Processing line... 926s Processing line... 926s TGACTCTTTAC 926s TGACTCTTTAC 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s AAGAGGCGGGGTAACATTC 926s AAGAGGCGGGGTAACATTC 926s Processing line... 926s Processing line... 926s AAGAGGCGGGG 926s AAGAGGCGGGG 926s Processing line... 926s Processing line... 926s ACAT 926s ACAT 926s Processing line... 926s ACAT 926s ACAT 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s ATGACTCTTTACACAAAGAGGCGGGGTA 926s ATGACTCTTTACACAAAGAGGCGGGGTA 926s Processing line... 926s ATGACTCTTTACACAA 926s ATGACTCTTTACACAA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s TGTACATGACTCTT 926s TGTACATGACTCTT 926s Processing line... 926s Processing line... 926s CATGACTCTTTACACAAAGAGGCGGGGT 926s CATGACTCTTTACACAAAGAGGCGGGGT 926s Processing line... 926s TACACAAAG 926s TACACAAAG 926s Processing line... 926s GGGGTAACATTCAGC 926s GGGGTAACATTCAGC 926s Processing line... 926s Processing line... 926s TGTACATGACT 926s TGTACATGACT 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s CATGACTC 926s CATGACTC 926s Processing line... 926s Processing line... 926s ATGACTCTTTACACAAAGA 926s ATGACTCTTTACACAAAGA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s --- Summary --- 926s Read 1 reference strings 926s Checked 39 alignments, 0 edits 926s --------------- 926s PASSED 926s Flattened IUPAC characters 926s Mutating sequence Sim.pm.2 926s Introducing 9 SNPs, 0/0 ref/read gaps, and 1 rearrangements 926s Finished SNPs 926s *** Run 79 of 100 926s /usr/bin/bowtie2 --rdg 31.1456917279325,11.6398465365111 --trim3 9 --rfg 27.3117476135951,17.93982965261 -k 10 --score-min L,6.10079207996248,6.56749331543079 --cp-min 3 --np 5 -N 0 -L19 --cp-ival 1 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq 926s Finished ref gaps 926s Finished read gaps 926s Mutating sequence Sim.pm.1 926s Introducing 3 SNPs, 0/0 ref/read gaps, and 3 rearrangements 926s Finished SNPs 926s Finished ref gaps 926s Finished read gaps 926s Mutated reference genome to subject genome 926s SNPs introduced: 12 926s Reference gaps introduced: 0 926s Read gaps introduced: 0 926s Rearrangements introduced: 4 926s Created read sampler 926s Sampling 67 reads 926s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 926s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 926s parsing sequence Sim.pm.1... 926s parsing sequence Sim.pm.2... 926s Parsed 74 reference bases 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 926s 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 926s 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 926s Read 50 alignments... 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Read 100 alignments... 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 67 reads; of these: 926s 56 (83.58%) were paired; of these: 926s 55 (98.21%) aligned concordantly 0 times 926s 1 (1.79%) aligned concordantly exactly 1 time 926s 0 (0.00%) aligned concordantly >1 times 926s ---- 926s 55 pairs aligned concordantly 0 times; of these: 926s 0 (0.00%) aligned discordantly 1 time 926s ---- 926s 55 pairs aligned 0 times concordantly or discordantly; of these: 926s 110 mates make up the pairs; of these: 926s 97 (88.18%) aligned 0 times 926s 7 (6.36%) aligned exactly 1 time 926s 6 (5.45%) aligned >1 times 926s 11 (16.42%) were unpaired; of these: 926s 8 (72.73%) aligned 0 times 926s 2 (18.18%) aligned exactly 1 time 926s 1 (9.09%) aligned >1 times 926s 14.63% overall alignment rate 926s Read 150 alignments... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s CAAA 926s CAAA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s AGGG 926s AGGG 926s Processing line... 926s AGGG 926s AGGG 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s ATTCAGCT 926s ATTCAGCT 926s Processing line... 926s Processing line... 926s AA 926s AA 926s Processing line... 926s TT 926s TT 926s Processing line... 926s AA 926s AA 926s Processing line... 926s AA 926s AA 926s Processing line... 926s AA 926s AA 926s Processing line... 926s AA 926s AA 926s Processing line... 926s TT 926s TT 926s Processing line... 926s TT 926s TT 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s GC 926s GC 926s Processing line... 926s GC 926s GC 926s Processing line... 926s GC 926s GC 926s Processing line... 926s GC 926s GC 926s Processing line... 926s GC 926s GC 926s Processing line... 926s GC 926s GC 926s /usr/bin/bowtie2 --rdg 31.1456917279325,11.6398465365111 --trim3 9 --rfg 27.3117476135951,17.93982965261 -k 10 --score-min L,6.10079207996248,6.56749331543079 --cp-min 3 --np 5 -N 0 -L19 --cp-ival 1 --qseq -p 3 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 926s Processing line... 926s GC 926s GC 926s Processing line... 926s GC 926s GC 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s CAA 926s CAA 926s Processing line... 926s Processing line... 926s ACACAAAGAGGCGGGGTA 926s ACACAAAGAGGCGGGGTA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s CTC 926s CTC 926s Processing line... 926s GAG 926s GAG 926s Processing line... 926s GAG 926s GAG 926s Processing line... 926s Processing line... 926s GGGGTAACA 926s GGGGTAACA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s AGAGGCGGGGTAACATTCAG 926s AGAGGCGGGGTAACATTCAG 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s GGA 926s GGA 926s Processing line... 926s GGA 926s GGA 926s Processing line... 926s Processing line... 926s Processing line... 926s AC 926s AC 926s Processing line... 926s AC 926s AC 926s Processing line... 926s AC 926s AC 926s Processing line... 926s GT 926s GT 926s Processing line... 926s AC 926s AC 926s Processing line... 926s AC 926s AC 926s Processing line... 926s AC 926s AC 926s Processing line... 926s GT 926s GT 926s Processing line... 926s AC 926s AC 926s Processing line... 926s GT 926s GT 926s Processing line... 926s TTACACAAAGAGGCGGGGTAACATTCAGCTACC 926s TTACACAAAGAGGCGGGGTAACATTCAGCTACC 926s Processing line... 926s TTTACACAAAGAGGC 926s TTTACACAAAGAGGC 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s TCT 926s TCT 926s Processing line... 926s AGA 926s AGA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s GAGGCGGGGTAACA 926s GAGGCGGGGTAACA 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s Processing line... 926s AC 926s AC 926s Processing line... 926s AC 926s AC 926s Processing line... 926s GT 926s GT 926s Processing line... 926s AC 926s AC 926s Processing line... 926s AC 926s AC 926s Processing line... 926s AC 926s AC 926s Processing line... 926s AC 926s AC 926s Processing line... 926s GT 926s GT 926s Processing line... 926s GT 926s GT 926s Processing line... 926s AC 926s AC 926s Processing line... 926s Processing line... 926s Processing line... 926s --- Summary --- 926s Read 1 reference strings 926s Checked 54 alignments, 0 edits 926s --------------- 926s PASSED 926s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 926s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 926s 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 926s 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 926s 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 926s 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 926s 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 926s 67 reads; of these: 926s 56 (83.58%) were paired; of these: 926s 55 (98.21%) aligned concordantly 0 times 926s 1 (1.79%) aligned concordantly exactly 1 time 926s 0 (0.00%) aligned concordantly >1 times 926s ---- 926s 55 pairs aligned concordantly 0 times; of these: 926s 0 (0.00%) aligned discordantly 1 time 926s ---- 926s 55 pairs aligned 0 times concordantly or discordantly; of these: 926s 110 mates make up the pairs; of these: 926s 97 (88.18%) aligned 0 times 926s 7 (6.36%) aligned exactly 1 time 926s 6 (5.45%) aligned >1 times 926s 11 (16.42%) were unpaired; of these: 926s 8 (72.73%) aligned 0 times 926s 2 (18.18%) aligned exactly 1 time 926s 1 (9.09%) aligned >1 times 926s 14.63% overall alignment rate 926s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 926s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 926s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 926s Flattened IUPAC characters 926s Mutating sequence Sim.pm.2 926s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 926s Finished SNPs 926s Finished ref gaps 926s Finished read gaps 926s Mutating sequence Sim.pm.1 926s Introducing 6 SNPs, 0/0 ref/read gaps, and 2 rearrangements 926s Finished SNPs 926s Finished ref gaps 926s Finished read gaps 926s Mutated reference genome to subject genome 926s SNPs introduced: 16 926s Reference gaps introduced: 0 926s Read gaps introduced: 0 926s Rearrangements introduced: 2 926s Created read sampler 926s Sampling 109 reads 926s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 926s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 926s parsing sequence Sim.pm.1... 926s parsing sequence Sim.pm.2... 926s Parsed 74 reference bases 926s *** Run 80 of 100 926s /usr/bin/bowtie2 -a --rdg 17.4000409189628 --local --cp-min 2 --cp-ival 1 --mm --trim5 3 --rfg 22.1878317645591,18.0099866920378 --score-min L,9.50977413092312,7.11471052921861 --np 2 --norc -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw 927s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '17' because it was < 2 characters long 927s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 927s Warning: skipping mate #2 of read '43' because it was < 2 characters long 927s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '48' because it was < 2 characters long 927s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '51' because it was < 2 characters long 927s Read 50 alignments... 927s Read 100 alignments... 927s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '71' because it was < 2 characters long 927s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '73' because it was < 2 characters long 927s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '77' because it was < 2 characters long 927s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '79' because it was < 2 characters long 927s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '84' because it was < 2 characters long 927s 109 reads; of these: 927s 98 (89.91%) were paired; of these: 927s 98 (100.00%) aligned concordantly 0 times 927s 0 (0.00%) aligned concordantly exactly 1 time 927s 0 (0.00%) aligned concordantly >1 times 927s ---- 927s 98 pairs aligned concordantly 0 times; of these: 927s 0 (0.00%) aligned discordantly 1 time 927s ---- 927s 98 pairs aligned 0 times concordantly or discordantly; of these: 927s 196 mates make up the pairs; of these: 927s 196 (100.00%) aligned 0 times 927s 0 (0.00%) aligned exactly 1 time 927s 0 (0.00%) aligned >1 times 927s 11 (10.09%) were unpaired; of these: 927s 11 (100.00%) aligned 0 times 927s 0 (0.00%) aligned exactly 1 time 927s 0 (0.00%) aligned >1 times 927s 0.00% overall alignment rate 927s Read 150 alignments... 927s Read 200 alignments... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s --- Summary --- 927s Read 1 reference strings 927s Checked 0 alignments, 0 edits 927s --------------- 927s PASSED 927s ALSO checking that bowtie2 and bowtie2-align match up 927s /usr/bin/bowtie2 -a --rdg 17.4000409189628 --local --cp-min 2 --cp-ival 1 --mm --trim5 3 --rfg 22.1878317645591,18.0099866920378 --score-min L,9.50977413092312,7.11471052921861 --np 2 --norc -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 927s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '17' because it was < 2 characters long 927s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 927s Warning: skipping mate #2 of read '43' because it was < 2 characters long 927s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '48' because it was < 2 characters long 927s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '51' because it was < 2 characters long 927s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '71' because it was < 2 characters long 927s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '73' because it was < 2 characters long 927s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '77' because it was < 2 characters long 927s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '79' because it was < 2 characters long 927s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 927s Warning: skipping mate #1 of read '84' because it was < 2 characters long 927s 109 reads; of these: 927s 98 (89.91%) were paired; of these: 927s 98 (100.00%) aligned concordantly 0 times 927s 0 (0.00%) aligned concordantly exactly 1 time 927s 0 (0.00%) aligned concordantly >1 times 927s ---- 927s 98 pairs aligned concordantly 0 times; of these: 927s 0 (0.00%) aligned discordantly 1 time 927s ---- 927s 98 pairs aligned 0 times concordantly or discordantly; of these: 927s 196 mates make up the pairs; of these: 927s 196 (100.00%) aligned 0 times 927s 0 (0.00%) aligned exactly 1 time 927s 0 (0.00%) aligned >1 times 927s 11 (10.09%) were unpaired; of these: 927s 11 (100.00%) aligned 0 times 927s 0 (0.00%) aligned exactly 1 time 927s 0 (0.00%) aligned >1 times 927s 0.00% overall alignment rate 927s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 927s Flattened IUPAC characters 927s Mutating sequence Sim.pm.2 927s Introducing 13 SNPs, 1/1 ref/read gaps, and 0 rearrangements 927s Finished SNPs 927s Finished ref gaps 927s Finished read gaps 927s Mutating sequence Sim.pm.1 927s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 927s Finished SNPs 927s Finished ref gaps 927s Finished read gaps 927s Mutated reference genome to subject genome 927s SNPs introduced: 13 927s Reference gaps introduced: 1 927s Read gaps introduced: 2 927s Rearrangements introduced: 0 927s Created read sampler 927s Sampling 58 reads 927s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 927s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 927s parsing sequence Sim.pm.1... 927s parsing sequence Sim.pm.2... 927s Parsed 74 reference bases 927s *** Run 81 of 100 927s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 6 --score-min L,1.48642432379819,7.07533807140018 --ma 6.60391170407296 --trim5 1 -a -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 927s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 927s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 927s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 927s Warning: skipping read '20' because it was < 2 characters long 927s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 927s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 927s Warning: skipping read '23' because it was < 2 characters long 927s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 927s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 927s Warning: skipping read '37' because it was < 2 characters long 927s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 927s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 927s Warning: skipping read '58' because it was < 2 characters long 927s 58 reads; of these: 927s 58 (100.00%) were unpaired; of these: 927s 46 (79.31%) aligned 0 times 927s 8 (13.79%) aligned exactly 1 time 927s 4 (6.90%) aligned >1 times 927s 20.69% overall alignment rate 927s Read 50 alignments... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s GGCGATA 927s GGCGATA 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s CG 927s CG 927s Processing line... 927s CG 927s CG 927s Processing line... 927s CG 927s CG 927s Processing line... 927s CG 927s CG 927s Processing line... 927s CG 927s CG 927s Processing line... 927s CG 927s CG 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s AA 927s AA 927s Processing line... 927s TT 927s TT 927s Processing line... 927s AA 927s AA 927s Processing line... 927s TT 927s TT 927s Processing line... 927s AA 927s AA 927s Processing line... 927s AA 927s AA 927s Processing line... 927s TT 927s TT 927s Processing line... 927s AA 927s AA 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s AGAGGCGGGGTAACATTCAGC 927s AGAGGCGGGGTAACATTCAGC 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s Processing line... 927s Processing line... 927s GCGGGGTAAC 927s GCGGGGTAAC 927s Processing line... 927s GCGATAAGGG 927s GCGATAAGGG 927s Processing line... 927s Processing line... 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s GC 927s GC 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s CAAAGAGGCGGG 927s CAAAGAGGCGGG 927s Processing line... 927s Processing line... 927s AGGCGGGGTAACATT 927s AGGCGGGGTAACATT 927s Processing line... 927s Processing line... 927s Processing line... 927s GGGTAAC 927s GGGTAAC 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s Processing line... 927s ACTCT 927s ACTCT 927s Processing line... 927s Processing line... 927s --- Summary --- 927s Read 1 reference strings 927s Checked 38 alignments, 0 edits 927s --------------- 927s PASSED 927s ALSO checking that bowtie2 and bowtie2-align match up 927s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 6 --score-min L,1.48642432379819,7.07533807140018 --ma 6.60391170407296 --trim5 1 -a -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 927s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 927s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 927s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 927s Warning: skipping read '20' because it was < 2 characters long 927s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 927s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 927s Warning: skipping read '23' because it was < 2 characters long 927s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 927s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 927s Warning: skipping read '37' because it was < 2 characters long 927s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 927s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 927s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 927s Warning: skipping read '58' because it was < 2 characters long 927s 58 reads; of these: 927s 58 (100.00%) were unpaired; of these: 927s 46 (79.31%) aligned 0 times 927s 8 (13.79%) aligned exactly 1 time 927s 4 (6.90%) aligned >1 times 927s 20.69% overall alignment rate 927s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 927s Flattened IUPAC characters 927s Mutating sequence Sim.pm.2 927s Introducing 3 SNPs, 0/1 ref/read gaps, and 2 rearrangements 927s Finished SNPs 927s Finished ref gaps 927s Finished read gaps 927s Mutating sequence Sim.pm.1 927s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 927s Finished SNPs 927s Finished ref gaps 927s Finished read gaps 927s Mutated reference genome to subject genome 927s SNPs introduced: 7 927s Reference gaps introduced: 0 927s Read gaps introduced: 1 927s Rearrangements introduced: 2 927s Created read sampler 927s Sampling 118 reads 927s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 927s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 927s parsing sequence Sim.pm.1... 927s parsing sequence Sim.pm.2... 927s Parsed 74 reference bases 927s *** Run 82 of 100 927s /usr/bin/bowtie2 -D 6 --cp-ival 1 -R 1 --np 12 --cp-min 5 --score-min L,7.49851650762088,3.38726293710868 --n-ceil 0.841110721460735,0.648708902131886 --local --mp 7.2472274219684,6.02803879621592 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 928s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 928s Warning: skipping read '3' because it was < 2 characters long 928s Warning: skipping read '107' because length (1) <= # seed mismatches (0) 928s Warning: skipping read '107' because it was < 2 characters long 928s Warning: skipping read '116' because length (1) <= # seed mismatches (0) 928s Warning: skipping read '116' because it was < 2 characters long 928s 118 reads; of these: 928s 118 (100.00%) were unpaired; of these: 928s 118 (100.00%) aligned 0 times 928s 0 (0.00%) aligned exactly 1 time 928s 0 (0.00%) aligned >1 times 928s 0.00% overall alignment rate 928s Read 50 alignments... 928s Read 100 alignments... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s --- Summary --- 928s Read 1 reference strings 928s Checked 0 alignments, 0 edits 928s --------------- 928s PASSED 928s ALSO checking that bowtie2 and bowtie2-align match up 928s /usr/bin/bowtie2 -D 6 --cp-ival 1 -R 1 --np 12 --cp-min 5 --score-min L,7.49851650762088,3.38726293710868 --n-ceil 0.841110721460735,0.648708902131886 --local --mp 7.2472274219684,6.02803879621592 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 928s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 928s Warning: skipping read '3' because it was < 2 characters long 928s Warning: skipping read '107' because length (1) <= # seed mismatches (0) 928s Warning: skipping read '107' because it was < 2 characters long 928s Warning: skipping read '116' because length (1) <= # seed mismatches (0) 928s Warning: skipping read '116' because it was < 2 characters long 928s 118 reads; of these: 928s 118 (100.00%) were unpaired; of these: 928s 118 (100.00%) aligned 0 times 928s 0 (0.00%) aligned exactly 1 time 928s 0 (0.00%) aligned >1 times 928s 0.00% overall alignment rate 928s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 928s Flattened IUPAC characters 928s Mutating sequence Sim.pm.1 928s Introducing 5 SNPs, 1/0 ref/read gaps, and 1 rearrangements 928s Finished SNPs 928s Finished ref gaps 928s Finished read gaps 928s Mutating sequence Sim.pm.2 928s Introducing 13 SNPs, 1/1 ref/read gaps, and 2 rearrangements 928s Finished SNPs 928s Finished ref gaps 928s Finished read gaps 928s Mutated reference genome to subject genome 928s SNPs introduced: 18 928s Reference gaps introduced: 2 928s Read gaps introduced: 1 928s Rearrangements introduced: 3 928s Created read sampler 928s Sampling 73 reads 928s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 928s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 928s parsing sequence Sim.pm.1... 928s parsing sequence Sim.pm.2... 928s *** Run 83 of 100 928s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 3 -k 4 --mp 5.20456273918405,1.05263517725933 --trim3 7 --local --np 2 --n-ceil 1.00507051331503,1.01449755916013 --gbar 6 --score-min L,8.22179397421539,8.94906270628345 --trim5 0 --rfg 16.1460129387728,7.51978480544952 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq 928s Parsed 74 reference bases 928s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 928s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 928s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 928s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 928s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 928s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 928s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 928s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 928s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 928s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 928s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 928s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 928s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 928s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 928s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 928s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 928s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 928s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 928s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 928s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 928s Read 50 alignments... 928s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 928s Read 100 alignments... 928s 73 reads; of these: 928s 61 (83.56%) were paired; of these: 928s 61 (100.00%) aligned concordantly 0 times 928s 0 (0.00%) aligned concordantly exactly 1 time 928s 0 (0.00%) aligned concordantly >1 times 928s ---- 928s 61 pairs aligned concordantly 0 times; of these: 928s 0 (0.00%) aligned discordantly 1 time 928s ---- 928s 61 pairs aligned 0 times concordantly or discordantly; of these: 928s 122 mates make up the pairs; of these: 928s 122 (100.00%) aligned 0 times 928s 0 (0.00%) aligned exactly 1 time 928s 0 (0.00%) aligned >1 times 928s 12 (16.44%) were unpaired; of these: 928s 12 (100.00%) aligned 0 times 928s 0 (0.00%) aligned exactly 1 time 928s 0 (0.00%) aligned >1 times 928s 0.00% overall alignment rate 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s --- Summary --- 928s Read 1 reference strings 928s Checked 0 alignments, 0 edits 928s --------------- 928s PASSED 928s Flattened IUPAC characters 928s Mutating sequence Sim.pm.1 928s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 928s Finished SNPs 928s Finished ref gaps 928s Finished read gaps 928s Mutating sequence Sim.pm.2 928s Introducing 6 SNPs, 1/2 ref/read gaps, and 0 rearrangements 928s Finished SNPs 928s Finished ref gaps 928s Finished read gaps 928s Mutated reference genome to subject genome 928s SNPs introduced: 7 928s Reference gaps introduced: 1 928s Read gaps introduced: 3 928s Rearrangements introduced: 0 928s Created read sampler 928s Sampling 76 reads 928s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 928s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 928s parsing sequence Sim.pm.1... 928s parsing sequence Sim.pm.2... 928s Parsed 74 reference bases 928s *** Run 84 of 100 928s /usr/bin/bowtie2 -k 3 --local --rdg 14.6334258945851 --cp-ival 1 --cp-min 4 --score-min L,8.60164387856598,6.8253694540618 --rfg 48.840288808767,8.40690025947361 -R 1 --norc -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 928s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 928s Warning: skipping mate #2 of read '20' because it was < 2 characters long 928s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read '23' because it was < 2 characters long 928s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read '37' because it was < 2 characters long 928s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read '41' because it was < 2 characters long 928s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read '48' because it was < 2 characters long 928s Read 50 alignments... 928s Read 100 alignments... 928s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 928s Warning: skipping mate #1 of read '75' because it was < 2 characters long 928s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 928s Warning: skipping mate #2 of read '76' because it was < 2 characters long 928s 76 reads; of these: 928s 76 (100.00%) were paired; of these: 928s 76 (100.00%) aligned concordantly 0 times 928s /usr/bin/bowtie2 -k 3 --local --rdg 14.6334258945851 --cp-ival 1 --cp-min 4 --score-min L,8.60164387856598,6.8253694540618 --rfg 48.840288808767,8.40690025947361 -R 1 --norc -f -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 928s 0 (0.00%) aligned concordantly exactly 1 time 928s 0 (0.00%) aligned concordantly >1 times 928s ---- 928s 76 pairs aligned concordantly 0 times; of these: 928s 0 (0.00%) aligned discordantly 1 time 928s ---- 928s 76 pairs aligned 0 times concordantly or discordantly; of these: 928s 152 mates make up the pairs; of these: 928s 152 (100.00%) aligned 0 times 928s 0 (0.00%) aligned exactly 1 time 928s 0 (0.00%) aligned >1 times 928s 0.00% overall alignment rate 928s Read 150 alignments... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s Processing line... 928s --- Summary --- 928s Read 1 reference strings 928s Checked 0 alignments, 0 edits 928s --------------- 928s PASSED 928s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 929s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 929s Warning: skipping mate #2 of read '20' because it was < 2 characters long 929s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 929s Warning: skipping mate #1 of read '23' because it was < 2 characters long 929s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (0) 929s Warning: skipping mate #1 of read '37' because it was < 2 characters long 929s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 929s Warning: skipping mate #1 of read '41' because it was < 2 characters long 929s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 929s Warning: skipping mate #1 of read '48' because it was < 2 characters long 929s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 929s Warning: skipping mate #1 of read '75' because it was < 2 characters long 929s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 929s Warning: skipping mate #2 of read '76' because it was < 2 characters long 929s 76 reads; of these: 929s 76 (100.00%) were paired; of these: 929s 76 (100.00%) aligned concordantly 0 times 929s 0 (0.00%) aligned concordantly exactly 1 time 929s 0 (0.00%) aligned concordantly >1 times 929s ---- 929s 76 pairs aligned concordantly 0 times; of these: 929s 0 (0.00%) aligned discordantly 1 time 929s ---- 929s 76 pairs aligned 0 times concordantly or discordantly; of these: 929s 152 mates make up the pairs; of these: 929s 152 (100.00%) aligned 0 times 929s 0 (0.00%) aligned exactly 1 time 929s 0 (0.00%) aligned >1 times 929s 0.00% overall alignment rate 929s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 929s Flattened IUPAC characters 929s Mutating sequence Sim.pm.2 929s Introducing 4 SNPs, 0/0 ref/read gaps, and 2 rearrangements 929s Finished SNPs 929s Finished ref gaps 929s Finished read gaps 929s Mutating sequence Sim.pm.1 929s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 929s Finished SNPs 929s Finished ref gaps 929s Finished read gaps 929s Mutated reference genome to subject genome 929s SNPs introduced: 5 929s Reference gaps introduced: 0 929s Read gaps introduced: 1 929s Rearrangements introduced: 2 929s Created read sampler 929s Sampling 20 reads 929s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 929s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 929s parsing sequence Sim.pm.1... 929s parsing sequence Sim.pm.2... 929s Parsed 74 reference bases 929s *** Run 85 of 100 929s /usr/bin/bowtie2 --ma 21.1455415037326 --score-min L,4.90851837500188,4.12763653641991 --gbar 3 --trim3 6 --rdg 48.0575611986652 --rfg 16.5041628749361 --cp-ival 2 --mm --cp-min 6 --np 3 -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 929s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 929s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 929s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 929s Warning: skipping read '1' because it was < 2 characters long 929s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 929s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 929s Warning: skipping read '2' because it was < 2 characters long 929s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 929s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 929s Warning: skipping read '3' because it was < 2 characters long 929s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 929s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 929s Warning: skipping read '8' because it was < 2 characters long 929s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 929s 20 reads; of these: 929s 20 (100.00%) were unpaired; of these: 929s 19 (95.00%) aligned 0 times 929s 1 (5.00%) aligned exactly 1 time 929s 0 (0.00%) aligned >1 times 929s 5.00% overall alignment rate 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s CATGACTCTTTACACAAAGA 929s CATGACTCTTTACACAAAGA 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s --- Summary --- 929s Read 1 reference strings 929s Checked 1 alignments, 0 edits 929s --------------- 929s PASSED 929s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 929s /usr/bin/bowtie2 --ma 21.1455415037326 --score-min L,4.90851837500188,4.12763653641991 --gbar 3 --trim3 6 --rdg 48.0575611986652 --rfg 16.5041628749361 --cp-ival 2 --mm --cp-min 6 --np 3 -r -p 3 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 929s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 929s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 929s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 929s Warning: skipping read '1' because it was < 2 characters long 929s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 929s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 929s Warning: skipping read '2' because it was < 2 characters long 929s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 929s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 929s Warning: skipping read '3' because it was < 2 characters long 929s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 929s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 929s Warning: skipping read '8' because it was < 2 characters long 929s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 929s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 929s 20 reads; of these: 929s 20 (100.00%) were unpaired; of these: 929s 19 (95.00%) aligned 0 times 929s 1 (5.00%) aligned exactly 1 time 929s 0 (0.00%) aligned >1 times 929s 5.00% overall alignment rate 929s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 929s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 929s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 929s Flattened IUPAC characters 929s Mutating sequence Sim.pm.1 929s Introducing 2 SNPs, 0/2 ref/read gaps, and 2 rearrangements 929s Finished SNPs 929s Finished ref gaps 929s Finished read gaps 929s Mutating sequence Sim.pm.2 929s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 929s Finished SNPs 929s Finished ref gaps 929s Finished read gaps 929s Mutated reference genome to subject genome 929s SNPs introduced: 8 929s Reference gaps introduced: 0 929s Read gaps introduced: 2 929s Rearrangements introduced: 3 929s Created read sampler 929s Sampling 32 reads 929s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 929s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 929s parsing sequence Sim.pm.1... 929s parsing sequence Sim.pm.2... 929s Parsed 74 reference bases 929s *** Run 86 of 100 929s /usr/bin/bowtie2 --trim5 4 --n-ceil 0.405474708399433,1.20774787438967 --score-min L,8.95420959317489,3.26791533491239 -D 7 --trim3 5 --rdg 33.8920343331168 --local --cp-min 5 --cp-ival 2 --mm -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw 929s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 929s Warning: skipping mate #1 of read '0' because it was < 2 characters long 929s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 929s Warning: skipping mate #2 of read '9' because it was < 2 characters long 929s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 929s Warning: skipping mate #1 of read '16' because it was < 2 characters long 929s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 929s Warning: skipping mate #1 of read '20' because it was < 2 characters long 929s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 929s Warning: skipping mate #1 of read '25' because it was < 2 characters long 929s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 929s Warning: skipping mate #2 of read '28' because it was < 2 characters long 929s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 929s Warning: skipping mate #1 of read '31' because it was < 2 characters long 929s 32 reads; of these: 929s 28 (87.50%) were paired; of these: 929s 28 (100.00%) aligned concordantly 0 times 929s 0 (0.00%) aligned concordantly exactly 1 time 929s 0 (0.00%) aligned concordantly >1 times 929s ---- 929s 28 pairs aligned concordantly 0 times; of these: 929s 0 (0.00%) aligned discordantly 1 time 929s ---- 929s 28 pairs aligned 0 times concordantly or discordantly; of these: 929s 56 mates make up the pairs; of these: 929s 56 (100.00%) aligned 0 times 929s 0 (0.00%) aligned exactly 1 time 929s 0 (0.00%) aligned >1 times 929s 4 (12.50%) were unpaired; of these: 929s 4 (100.00%) aligned 0 times 929s 0 (0.00%) aligned exactly 1 time 929s 0 (0.00%) aligned >1 times 929s 0.00% overall alignment rate 929s Read 50 alignments... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s Processing line... 929s --- Summary --- 929s Read 1 reference strings 929s Checked 0 alignments, 0 edits 929s --------------- 929s PASSED 929s ALSO checking that bowtie2 and bowtie2-align match up 929s /usr/bin/bowtie2 --trim5 4 --n-ceil 0.405474708399433,1.20774787438967 --score-min L,8.95420959317489,3.26791533491239 -D 7 --trim3 5 --rdg 33.8920343331168 --local --cp-min 5 --cp-ival 2 --mm -r -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.raw -2 /tmp/Sim.pm.77cQkkTL_2.raw | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 930s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read '0' because it was < 2 characters long 930s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 930s Warning: skipping mate #2 of read '9' because it was < 2 characters long 930s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read '16' because it was < 2 characters long 930s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read '20' because it was < 2 characters long 930s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read '25' because it was < 2 characters long 930s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 930s Warning: skipping mate #2 of read '28' because it was < 2 characters long 930s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read '31' because it was < 2 characters long 930s 32 reads; of these: 930s 28 (87.50%) were paired; of these: 930s 28 (100.00%) aligned concordantly 0 times 930s 0 (0.00%) aligned concordantly exactly 1 time 930s 0 (0.00%) aligned concordantly >1 times 930s ---- 930s 28 pairs aligned concordantly 0 times; of these: 930s 0 (0.00%) aligned discordantly 1 time 930s ---- 930s 28 pairs aligned 0 times concordantly or discordantly; of these: 930s 56 mates make up the pairs; of these: 930s 56 (100.00%) aligned 0 times 930s 0 (0.00%) aligned exactly 1 time 930s 0 (0.00%) aligned >1 times 930s 4 (12.50%) were unpaired; of these: 930s 4 (100.00%) aligned 0 times 930s 0 (0.00%) aligned exactly 1 time 930s 0 (0.00%) aligned >1 times 930s 0.00% overall alignment rate 930s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 930s Flattened IUPAC characters 930s Mutating sequence Sim.pm.2 930s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 930s Finished SNPs 930s Finished ref gaps 930s Finished read gaps 930s Mutating sequence Sim.pm.1 930s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 930s Finished SNPs 930s Finished ref gaps 930s Finished read gaps 930s Mutated reference genome to subject genome 930s SNPs introduced: 6 930s Reference gaps introduced: 0 930s Read gaps introduced: 1 930s Rearrangements introduced: 1 930s Created read sampler 930s Sampling 169 reads 930s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 930s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 930s parsing sequence Sim.pm.1... 930s parsing sequence Sim.pm.2... 930s Parsed 74 reference bases 930s *** Run 87 of 100 930s /usr/bin/bowtie2 --ma 11.5980395846224 --rdg 26.9252662196046,10.3276849472212 --mp 5.45243919568944,3.43777004126946 --trim3 6 --cp-ival 1 --cp-min 12 --gbar 5 --score-min L,3.5927418020475,8.8808615421286 --n-ceil 0.468785030463118,0.969679043359458 --rfg 35.4241438340639,1.47836426815994 -R 4 --qseq -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.qseq -2 /tmp/Sim.pm.77cQkkTL_2.qseq 930s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #2 of read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 930s Warning: skipping mate #2 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 930s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Read 50 alignments... 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Read 100 alignments... 930s Read 150 alignments... 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #2 of read 'R_1_1_1_123_123_1/1' because length (1) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 930s Warning: skipping mate #2 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 930s 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 930s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 930s 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 930s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_137_137_1/1' because length (1) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #2 of read 'R_1_1_1_142_142_1/1' because length (1) <= # seed mismatches (0) 930s Warning: skipping mate #2 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_149_149_1/1' because length (1) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_149_149_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_151_151_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_160_160_1/1' because length (0) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_160_160_1/1' because it was < 2 characters long 930s 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 930s 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 930s Read 200 alignments... 930s Read 250 alignments... 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping mate #1 of read 'R_1_1_1_165_165_1/1' because length (1) <= # seed mismatches (0) 930s Warning: skipping mate #1 of read 'R_1_1_1_165_165_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Read 300 alignments... 930s 169 reads; of these: 930s 151 (89.35%) were paired; of these: 930s 150 (99.34%) aligned concordantly 0 times 930s 0 (0.00%) aligned concordantly exactly 1 time 930s 1 (0.66%) aligned concordantly >1 times 930s ---- 930s 150 pairs aligned concordantly 0 times; of these: 930s 2 (1.33%) aligned discordantly 1 time 930s ---- 930s 148 pairs aligned 0 times concordantly or discordantly; of these: 930s 296 mates make up the pairs; of these: 930s 247 (83.45%) aligned 0 times 930s 38 (12.84%) aligned exactly 1 time 930s 11 (3.72%) aligned >1 times 930s 18 (10.65%) were unpaired; of these: 930s 16 (88.89%) aligned 0 times 930s 2 (11.11%) aligned exactly 1 time 930s 0 (0.00%) aligned >1 times 930s 17.81% overall alignment rate 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s AAAGAGGCGGGG 930s AAAGAGGCGGGG 930s Processing line... 930s ACATGACTCTTTA 930s ACATGACTCTTTA 930s Processing line... 930s TACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGC 930s TACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGC 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s TGTACATGA 930s TGTACATGA 930s Processing line... 930s Processing line... 930s ATGACTCTTTACAC 930s ATGACTCTTTACAC 930s Processing line... 930s Processing line... 930s TACACAAAGAGGCGGGGTA 930s TACACAAAGAGGCGGGGTA 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s CATGAC 930s CATGAC 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GGTAACAT 930s GGTAACAT 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s CTTTA 930s CTTTA 930s Processing line... 930s Processing line... 930s GACTCTTTACACAAAGAGGCGGGGTAACATTCAGC 930s GACTCTTTACACAAAGAGGCGGGGTAACATTCAGC 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GG 930s GG 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s CTT 930s CTT 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GACTCTT 930s GACTCTT 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s AAGAGGCGGGGTAACATTCAG 930s AAGAGGCGGGGTAACATTCAG 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s TCTTTACACA 930s TCTTTACACA 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s ACACAAAGAG 930s ACACAAAGAG 930s Processing line... 930s ACAC 930s ACAC 930s Processing line... 930s Processing line... 930s Processing line... 930s GGTG 930s GGTG 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s AGAGGC 930s AGAGGC 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s TTACACA 930s TTACACA 930s Processing line... 930s Processing line... 930s CACAAAGAG 930s CACAAAGAG 930s Processing line... 930s Processing line... 930s GG 930s GG 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GTACATGACTCTTTACACAA 930s GTACATGACTCTTTACACAA 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GGTAACATTC 930s GGTAACATTC 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GCGGGGTAACATTCAGCTACC 930s GCGGGGTAACATTCAGCTACC 930s Processing line... 930s Processing line... 930s AAGAGGCGGGGT 930s AAGAGGCGGGGT 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s ACAAA 930s ACAAA 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s CAA 930s CAA 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s AA 930s AA 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GAT 930s GAT 930s Processing line... 930s AAAGAGGCGGGGTAAC 930s AAAGAGGCGGGGTAAC 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GGGTGTACATGACTCTT 930s GGGTGTACATGACTCTT 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GGGGTAACA 930s GGGGTAACA 930s Processing line... 930s Processing line... 930s TACATGA 930s TACATGA 930s Processing line... 930s Processing line... 930s TCTTTACACAAA 930s TCTTTACACAAA 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s TGACTCTTTACACAAAGAGGCGGGGTAACAT 930s TGACTCTTTACACAAAGAGGCGGGGTAACAT 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s TACATGACTCTT 930s TACATGACTCTT 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GACTCTTTACACAAAGAGGCGGG 930s GACTCTTTACACAAAGAGGCGGG 930s Processing line... 930s Processing line... 930s GCGGGG 930s GCGGGG 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s TAA 930s TAA 930s Processing line... 930s Processing line... 930s GACTCTTTACA 930s GACTCTTTACA 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s AA 930s AA 930s Processing line... 930s Processing line... 930s ACAAA 930s ACAAA 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s *** Run 88 of 100 930s /usr/bin/bowtie2 -a --rdg 32.8707568110034,18.4063111369202 --cp-min 6 --cp-ival 1 --trim5 0 --score-min L,5.53748332973853,3.97046421165087 --np 2 --norc --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq 930s Processing line... 930s Processing line... 930s Processing line... 930s CG 930s CG 930s Processing line... 930s GGCGGGGTAACATTCA 930s GGCGGGGTAACATTCA 930s Processing line... 930s Processing line... 930s Processing line... 930s ACTCTT 930s ACTCTT 930s Processing line... 930s Processing line... 930s TGACTCTTTACACAAAGAGGCGGGGTAACATTCAG 930s TGACTCTTTACACAAAGAGGCGGGGTAACATTCAG 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s CTCTTTACACAAAGAGGC 930s CTCTTTACACAAAGAGGC 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GG 930s GG 930s Processing line... 930s Processing line... 930s AAA 930s AAA 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s CTTTACACAAAG 930s CTTTACACAAAG 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s CGGG 930s CGGG 930s Processing line... 930s Processing line... 930s Processing line... 930s CAGC 930s CAGC 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GACTCTTTACACAAAGAGGCGGGGTAAC 930s GACTCTTTACACAAAGAGGCGGGGTAAC 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s TGACTCTTTACACAAAGAGGCGGGGT 930s TGACTCTTTACACAAAGAGGCGGGGT 930s Processing line... 930s Processing line... 930s CTCTT 930s CTCTT 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s AG 930s AG 930s Processing line... 930s Processing line... 930s --- Summary --- 930s Read 1 reference strings 930s Checked 57 alignments, 0 edits 930s --------------- 930s PASSED 930s Flattened IUPAC characters 930s Mutating sequence Sim.pm.2 930s Introducing 14 SNPs, 0/0 ref/read gaps, and 1 rearrangements 930s Finished SNPs 930s Finished ref gaps 930s Finished read gaps 930s Mutating sequence Sim.pm.1 930s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 930s Finished SNPs 930s Finished ref gaps 930s Finished read gaps 930s Mutated reference genome to subject genome 930s SNPs introduced: 17 930s Reference gaps introduced: 0 930s Read gaps introduced: 0 930s Rearrangements introduced: 1 930s Created read sampler 930s Sampling 48 reads 930s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.qseq & /tmp/Sim.pm.77cQkkTL_2.qseq 930s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 930s parsing sequence Sim.pm.1... 930s parsing sequence Sim.pm.2... 930s Parsed 74 reference bases 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 930s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s 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 930s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 930s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 930s 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 930s 48 reads; of these: 930s 48 (100.00%) were unpaired; of these: 930s 45 (93.75%) aligned 0 times 930s 0 (0.00%) aligned exactly 1 time 930s 3 (6.25%) aligned >1 times 930s 6.25% overall alignment rate 930s Read 50 alignments... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s TT 930s TT 930s Processing line... 930s TT 930s TT 930s Processing line... 930s TT 930s TT 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s GG 930s GG 930s Processing line... 930s GG 930s GG 930s Processing line... 930s GG 930s GG 930s Processing line... 930s GG 930s GG 930s Processing line... 930s GG 930s GG 930s Processing line... 930s GG 930s GG 930s Processing line... 930s GG 930s GG 930s Processing line... 930s GG 930s GG 930s Processing line... 930s GG 930s GG 930s Processing line... 930s GG 930s GG 930s Processing line... 930s /usr/bin/bowtie2 -a --rdg 32.8707568110034,18.4063111369202 --cp-min 6 --cp-ival 1 --trim5 0 --score-min L,5.53748332973853,3.97046421165087 --np 2 --norc --qseq -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 930s GG 930s GG 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s TG 930s TG 930s Processing line... 930s TG 930s TG 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s Processing line... 930s --- Summary --- 930s Read 1 reference strings 930s Checked 16 alignments, 0 edits 930s --------------- 930s PASSED 930s ALSO checking that bowtie2 and bowtie2-align match up 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 931s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 931s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 931s 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 931s 48 reads; of these: 931s 48 (100.00%) were unpaired; of these: 931s 45 (93.75%) aligned 0 times 931s 0 (0.00%) aligned exactly 1 time 931s 3 (6.25%) aligned >1 times 931s 6.25% overall alignment rate 931s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 931s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 931s /usr/bin/bowtie2 -a --rdg 32.8707568110034,18.4063111369202 --cp-min 6 --cp-ival 1 --trim5 0 --score-min L,5.53748332973853,3.97046421165087 --np 2 --norc --qseq -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 931s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s 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 931s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 931s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 931s 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 931s 48 reads; of these: 931s 48 (100.00%) were unpaired; of these: 931s 45 (93.75%) aligned 0 times 931s 0 (0.00%) aligned exactly 1 time 931s 3 (6.25%) aligned >1 times 931s 6.25% overall alignment rate 931s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 931s Flattened IUPAC characters 931s Mutating sequence Sim.pm.1 931s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 931s Finished SNPs 931s Finished ref gaps 931s Finished read gaps 931s Mutating sequence Sim.pm.2 931s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 931s Finished SNPs 931s Finished ref gaps 931s Finished read gaps 931s Mutated reference genome to subject genome 931s SNPs introduced: 5 931s Reference gaps introduced: 1 931s Read gaps introduced: 0 931s Rearrangements introduced: 2 931s Created read sampler 931s Sampling 85 reads 931s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 931s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 931s *** Run 89 of 100 931s /usr/bin/bowtie2 --trim5 7 --n-ceil 1.09147582658354,0.85232863712494 --score-min L,7.32138317419103,1.80763846712619 --nofw -N 0 -L16 --trim3 6 --mp 6.39808278709512,3.54266929120146 --rdg 33.1585010688159 --local -M 8 --cp-min 2 --cp-ival 3 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 931s parsing sequence Sim.pm.1... 931s parsing sequence Sim.pm.2... 931s Parsed 74 reference bases 931s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 931s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '3' because it was < 2 characters long 931s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '5' because it was < 2 characters long 931s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '12' because it was < 2 characters long 931s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '13' because it was < 2 characters long 931s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '15' because it was < 2 characters long 931s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '19' because it was < 2 characters long 931s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '21' because it was < 2 characters long 931s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '23' because it was < 2 characters long 931s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '25' because it was < 2 characters long 931s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '28' because it was < 2 characters long 931s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '29' because it was < 2 characters long 931s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '36' because it was < 2 characters long 931s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '43' because it was < 2 characters long 931s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '50' because it was < 2 characters long 931s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '51' because it was < 2 characters long 931s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '52' because it was < 2 characters long 931s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '60' because it was < 2 characters long 931s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '62' because it was < 2 characters long 931s Read 50 alignments... 931s Read 100 alignments... 931s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '66' because it was < 2 characters long 931s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '70' because it was < 2 characters long 931s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '78' because it was < 2 characters long 931s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '79' because it was < 2 characters long 931s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '84' because it was < 2 characters long 931s 85 reads; of these: 931s 68 (80.00%) were paired; of these: 931s 68 (100.00%) aligned concordantly 0 times 931s 0 (0.00%) aligned concordantly exactly 1 time 931s 0 (0.00%) aligned concordantly >1 times 931s ---- 931s 68 pairs aligned concordantly 0 times; of these: 931s 0 (0.00%) aligned discordantly 1 time 931s ---- 931s 68 pairs aligned 0 times concordantly or discordantly; of these: 931s 136 mates make up the pairs; of these: 931s 136 (100.00%) aligned 0 times 931s 0 (0.00%) aligned exactly 1 time 931s 0 (0.00%) aligned >1 times 931s 17 (20.00%) were unpaired; of these: 931s 17 (100.00%) aligned 0 times 931s 0 (0.00%) aligned exactly 1 time 931s 0 (0.00%) aligned >1 times 931s 0.00% overall alignment rate 931s Read 150 alignments... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s Processing line... 931s --- Summary --- 931s Read 1 reference strings 931s Checked 0 alignments, 0 edits 931s --------------- 931s PASSED 931s ALSO checking that bowtie2 and bowtie2-align match up 931s /usr/bin/bowtie2 --trim5 7 --n-ceil 1.09147582658354,0.85232863712494 --score-min L,7.32138317419103,1.80763846712619 --nofw -N 0 -L16 --trim3 6 --mp 6.39808278709512,3.54266929120146 --rdg 33.1585010688159 --local -M 8 --cp-min 2 --cp-ival 3 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 931s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 931s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '3' because it was < 2 characters long 931s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '5' because it was < 2 characters long 931s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '12' because it was < 2 characters long 931s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '13' because it was < 2 characters long 931s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '15' because it was < 2 characters long 931s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '19' because it was < 2 characters long 931s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '21' because it was < 2 characters long 931s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '23' because it was < 2 characters long 931s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '25' because it was < 2 characters long 931s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '28' because it was < 2 characters long 931s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '29' because it was < 2 characters long 931s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '36' because it was < 2 characters long 931s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '43' because it was < 2 characters long 931s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '50' because it was < 2 characters long 931s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '51' because it was < 2 characters long 931s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '52' because it was < 2 characters long 931s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '60' because it was < 2 characters long 931s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 931s Warning: skipping read '62' because it was < 2 characters long 931s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '66' because it was < 2 characters long 931s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '70' because it was < 2 characters long 931s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '78' because it was < 2 characters long 931s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '79' because it was < 2 characters long 931s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 931s Warning: skipping mate #1 of read '84' because it was < 2 characters long 931s 85 reads; of these: 931s 68 (80.00%) were paired; of these: 931s 68 (100.00%) aligned concordantly 0 times 931s 0 (0.00%) aligned concordantly exactly 1 time 931s 0 (0.00%) aligned concordantly >1 times 931s ---- 931s 68 pairs aligned concordantly 0 times; of these: 931s 0 (0.00%) aligned discordantly 1 time 931s ---- 931s 68 pairs aligned 0 times concordantly or discordantly; of these: 931s 136 mates make up the pairs; of these: 931s 136 (100.00%) aligned 0 times 931s 0 (0.00%) aligned exactly 1 time 931s 0 (0.00%) aligned >1 times 931s 17 (20.00%) were unpaired; of these: 931s 17 (100.00%) aligned 0 times 931s 0 (0.00%) aligned exactly 1 time 931s 0 (0.00%) aligned >1 times 931s 0.00% overall alignment rate 931s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 931s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 931s /usr/bin/bowtie2 --trim5 7 --n-ceil 1.09147582658354,0.85232863712494 --score-min L,7.32138317419103,1.80763846712619 --nofw -N 0 -L16 --trim3 6 --mp 6.39808278709512,3.54266929120146 --rdg 33.1585010688159 --local -M 8 --cp-min 2 --cp-ival 3 -q -p 3 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 932s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 932s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 932s Warning: skipping read '3' because it was < 2 characters long 932s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 932s Warning: skipping read '5' because it was < 2 characters long 932s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 932s Warning: skipping read '12' because it was < 2 characters long 932s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '13' because it was < 2 characters long 932s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 932s Warning: skipping read '15' because it was < 2 characters long 932s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '50' because it was < 2 characters long 932s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '51' because it was < 2 characters long 932s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '52' because it was < 2 characters long 932s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '60' because it was < 2 characters long 932s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 932s Warning: skipping read '62' because it was < 2 characters long 932s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '19' because it was < 2 characters long 932s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '21' because it was < 2 characters long 932s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '23' because it was < 2 characters long 932s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '36' because it was < 2 characters long 932s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 932s Warning: skipping read '25' because it was < 2 characters long 932s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '28' because it was < 2 characters long 932s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '29' because it was < 2 characters long 932s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '84' because it was < 2 characters long 932s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '66' because it was < 2 characters long 932s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '70' because it was < 2 characters long 932s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '78' because it was < 2 characters long 932s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '79' because it was < 2 characters long 932s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '43' because it was < 2 characters long 932s 85 reads; of these: 932s 68 (80.00%) were paired; of these: 932s 68 (100.00%) aligned concordantly 0 times 932s 0 (0.00%) aligned concordantly exactly 1 time 932s 0 (0.00%) aligned concordantly >1 times 932s ---- 932s 68 pairs aligned concordantly 0 times; of these: 932s 0 (0.00%) aligned discordantly 1 time 932s ---- 932s 68 pairs aligned 0 times concordantly or discordantly; of these: 932s 136 mates make up the pairs; of these: 932s 136 (100.00%) aligned 0 times 932s 0 (0.00%) aligned exactly 1 time 932s 0 (0.00%) aligned >1 times 932s 17 (20.00%) were unpaired; of these: 932s 17 (100.00%) aligned 0 times 932s 0 (0.00%) aligned exactly 1 time 932s 0 (0.00%) aligned >1 times 932s 0.00% overall alignment rate 932s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 932s Flattened IUPAC characters 932s Mutating sequence Sim.pm.2 932s Introducing 11 SNPs, 0/0 ref/read gaps, and 1 rearrangements 932s Finished SNPs 932s Finished ref gaps 932s Finished read gaps 932s Mutating sequence Sim.pm.1 932s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 932s Finished SNPs 932s Finished ref gaps 932s Finished read gaps 932s Mutated reference genome to subject genome 932s SNPs introduced: 11 932s Reference gaps introduced: 0 932s Read gaps introduced: 0 932s Rearrangements introduced: 1 932s Created read sampler 932s Sampling 94 reads 932s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 932s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 932s parsing sequence Sim.pm.1... 932s parsing sequence Sim.pm.2... 932s Parsed 74 reference bases 932s *** Run 90 of 100 932s /usr/bin/bowtie2 --rfg 26.7208798710605 --trim5 3 --score-min L,6.91464562795352,6.36401425532122 --n-ceil 0.109457567242856,0.861273247147084 --cp-min 2 --cp-ival 1 -a --mp 9.58668202667869,2.01520395665073 --ma 27.4243572871528 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 932s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 932s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '8' because it was < 2 characters long 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 932s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '21' because it was < 2 characters long 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 932s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '31' because it was < 2 characters long 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 932s Read 50 alignments... 932s Read 100 alignments... 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 932s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '61' because it was < 2 characters long 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 932s 94 reads; of these: 932s 90 (95.74%) were paired; of these: 932s 90 (100.00%) aligned concordantly 0 times 932s 0 (0.00%) aligned concordantly exactly 1 time 932s 0 (0.00%) aligned concordantly >1 times 932s ---- 932s 90 pairs aligned concordantly 0 times; of these: 932s 1 (1.11%) aligned discordantly 1 time 932s ---- 932s 89 pairs aligned 0 times concordantly or discordantly; of these: 932s 178 mates make up the pairs; of these: 932s 149 (83.71%) aligned 0 times 932s 21 (11.80%) aligned exactly 1 time 932s 8 (4.49%) aligned >1 times 932s 4 (4.26%) were unpaired; of these: 932s 3 (75.00%) aligned 0 times 932s 1 (25.00%) aligned exactly 1 time 932s 0 (0.00%) aligned >1 times 932s 17.39% overall alignment rate 932s Read 150 alignments... 932s Read 200 alignments... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s GGGTGTACATGACTCTTTAC 932s GGGTGTACATGACTCTTTAC 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s AAAGAGGCGGGGTAACATTCAG 932s AAAGAGGCGGGGTAACATTCAG 932s Processing line... 932s ACTCTTTACACAAAGAG 932s ACTCTTTACACAAAGAG 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s ACATGA 932s ACATGA 932s Processing line... 932s Processing line... 932s TCTTTACACAAAGA 932s TCTTTACACAAAGA 932s Processing line... 932s Processing line... 932s ACTCTTTACACAAAGAGGCGGGGTAACAT 932s ACTCTTTACACAAAGAGGCGGGGTAACAT 932s Processing line... 932s Processing line... 932s GGCG 932s GGCG 932s Processing line... 932s GGCG 932s GGCG 932s Processing line... 932s ACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCTA 932s ACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCTA 932s Processing line... 932s TTT 932s TTT 932s Processing line... 932s AAA 932s AAA 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s ATGACTCTTTACACAAAGAGGCGG 932s ATGACTCTTTACACAAAGAGGCGG 932s Processing line... 932s TTC 932s TTC 932s Processing line... 932s GAA 932s GAA 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s GTACATGACTCTTTACACAAAGAG 932s GTACATGACTCTTTACACAAAGAG 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s GGG 932s GGG 932s Processing line... 932s GGG 932s GGG 932s Processing line... 932s GGG 932s GGG 932s Processing line... 932s GGG 932s GGG 932s Processing line... 932s GGG 932s GGG 932s Processing line... 932s CGGGGTAACATTCAGCTA 932s CGGGGTAACATTCAGCTA 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s GGGTAACA 932s GGGTAACA 932s Processing line... 932s Processing line... 932s GCGGGGTAACA 932s GCGGGGTAACA 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s TGTACATGA 932s TGTACATGA 932s Processing line... 932s Processing line... 932s GTGTACAT 932s GTGTACAT 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s GGGTGTACAT 932s GGGTGTACAT 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s GTACATGAC 932s GTACATGAC 932s Processing line... 932s Processing line... 932s CAC 932s CAC 932s Processing line... 932s GTG 932s GTG 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s GGGTAACATTCAGCTA 932s GGGTAACATTCAGCTA 932s Processing line... 932s Processing line... 932s AGAGGCGGGGTA 932s AGAGGCGGGGTA 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s GGG 932s GGG 932s Processing line... 932s GGG 932s GGG 932s Processing line... 932s GGG 932s GGG 932s Processing line... 932s GGG 932s GGG 932s Processing line... 932s GGG 932s GGG 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s ATGACTCTTTACACAAA 932s ATGACTCTTTACACAAA 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s ATT 932s ATT 932s Processing line... 932s Processing line... 932s CTCTTTACACAAAGAGGCGGGGTA 932s CTCTTTACACAAAGAGGCGGGGTA 932s Processing line... 932s Processing line... 932s CACAAAGAGGCGGGG 932s CACAAAGAGGCGGGG 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s ATGAC 932s ATGAC 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s ACTCTTTACACAAAGAGGCGGGGTAACAT 932s ACTCTTTACACAAAGAGGCGGGGTAACAT 932s Processing line... 932s Processing line... 932s GA 932s GA 932s Processing line... 932s GA 932s GA 932s Processing line... 932s TC 932s TC 932s Processing line... 932s TC 932s TC 932s Processing line... 932s GA 932s GA 932s Processing line... 932s GA 932s GA 932s Processing line... 932s GA 932s GA 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s GAA 932s GAA 932s Processing line... 932s TTC 932s TTC 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s Processing line... 932s --- Summary --- 932s Read 1 reference strings 932s Checked 51 alignments, 0 edits 932s --------------- 932s PASSED 932s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 932s /usr/bin/bowtie2 --rfg 26.7208798710605 --trim5 3 --score-min L,6.91464562795352,6.36401425532122 --n-ceil 0.109457567242856,0.861273247147084 --cp-min 2 --cp-ival 1 -a --mp 9.58668202667869,2.01520395665073 --ma 27.4243572871528 -f -p 4 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 932s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 932s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '8' because it was < 2 characters long 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 932s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '61' because it was < 2 characters long 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 932s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '21' because it was < 2 characters long 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 932s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 932s Warning: skipping mate #1 of read '31' because it was < 2 characters long 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 932s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 932s 94 reads; of these: 932s 90 (95.74%) were paired; of these: 932s 90 (100.00%) aligned concordantly 0 times 932s 0 (0.00%) aligned concordantly exactly 1 time 932s 0 (0.00%) aligned concordantly >1 times 932s ---- 932s 90 pairs aligned concordantly 0 times; of these: 932s 1 (1.11%) aligned discordantly 1 time 932s ---- 932s 89 pairs aligned 0 times concordantly or discordantly; of these: 932s 178 mates make up the pairs; of these: 932s 149 (83.71%) aligned 0 times 932s 21 (11.80%) aligned exactly 1 time 932s 8 (4.49%) aligned >1 times 932s 4 (4.26%) were unpaired; of these: 932s 3 (75.00%) aligned 0 times 932s 1 (25.00%) aligned exactly 1 time 932s 0 (0.00%) aligned >1 times 932s 17.39% overall alignment rate 932s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 932s Flattened IUPAC characters 932s Mutating sequence Sim.pm.2 932s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 932s Finished SNPs 932s Finished ref gaps 932s Finished read gaps 932s Mutating sequence Sim.pm.1 932s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 932s Finished SNPs 932s Finished ref gaps 932s Finished read gaps 932s Mutated reference genome to subject genome 932s SNPs introduced: 7 932s Reference gaps introduced: 1 932s Read gaps introduced: 1 932s Rearrangements introduced: 0 932s Created read sampler 932s Sampling 90 reads 932s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 932s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 932s parsing sequence Sim.pm.1... 932s parsing sequence Sim.pm.2... 932s Parsed 74 reference bases 932s *** Run 91 of 100 932s /usr/bin/bowtie2 --norc --cp-min 5 --cp-ival 2 --trim5 0 --mp 6.23564523133908,4.18995661760974 --score-min L,5.18569394284114,4.3845798907286 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 933s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '4' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 933s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '10' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 933s Read 50 alignments... 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 933s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '66' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 933s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '72' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 933s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #1 of read '85' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 933s 90 reads; of these: 933s 90 (100.00%) were paired; of these: 933s 89 (98.89%) aligned concordantly 0 times 933s 0 (0.00%) aligned concordantly exactly 1 time 933s 1 (1.11%) aligned concordantly >1 times 933s ---- 933s 89 pairs aligned concordantly 0 times; of these: 933s 0 (0.00%) aligned discordantly 1 time 933s ---- 933s 89 pairs aligned 0 times concordantly or discordantly; of these: 933s 178 mates make up the pairs; of these: 933s 160 (89.89%) aligned 0 times 933s 11 (6.18%) aligned exactly 1 time 933s 7 (3.93%) aligned >1 times 933s 11.11% overall alignment rate 933s Read 100 alignments... 933s Read 150 alignments... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s CTCTT 933s CTCTT 933s Processing line... 933s GT 933s GT 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s AAGAG 933s AAGAG 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s ACA 933s ACA 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s ACATGACTCTTTACACAAAGAGGCGGGGTAACA 933s ACATGACTCTTTACACAAAGAGGCGGGGTAACA 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s GGGTGTACATGACTCTTTACACAAAGAGGCGGGGT 933s GGGTGTACATGACTCTTTACACAAAGAGGCGGGGT 933s Processing line... 933s Processing line... 933s GTGTACATGACTCTTTACACAAAGAGGCGGG 933s GTGTACATGACTCTTTACACAAAGAGGCGGG 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s CTTTACACAAAGAGG 933s CTTTACACAAAGAGG 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s ACATG 933s ACATG 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s AT 933s AT 933s Processing line... 933s Processing line... 933s TCTTTACACAAAGAGGCGGGGTA 933s TCTTTACACAAAGAGGCGGGGTA 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s /usr/bin/bowtie2 --norc --cp-min 5 --cp-ival 2 --trim5 0 --mp 6.23564523133908,4.18995661760974 --score-min L,5.18569394284114,4.3845798907286 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 933s Processing line... 933s Processing line... 933s AAG 933s AAG 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s CC 933s CC 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s GGGTGTACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCT 933s GGGTGTACATGACTCTTTACACAAAGAGGCGGGGTAACATTCAGCT 933s Processing line... 933s Processing line... 933s CC 933s CC 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s ACAAAGAGGCGGGGTAACATTCAGC 933s ACAAAGAGGCGGGGTAACATTCAGC 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s AGAGGCGGGG 933s AGAGGCGGGG 933s Processing line... 933s Processing line... 933s AC 933s AC 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s GGTGTACATG 933s GGTGTACATG 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s Processing line... 933s TG 933s TG 933s Processing line... 933s Processing line... 933s Processing line... 933s --- Summary --- 933s Read 1 reference strings 933s Checked 20 alignments, 0 edits 933s --------------- 933s PASSED 933s ALSO checking that bowtie2 and bowtie2-align match up 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 933s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '4' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 933s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '10' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 933s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '66' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 933s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '72' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 933s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #1 of read '85' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 933s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 933s /usr/bin/bowtie2 --norc --cp-min 5 --cp-ival 2 --trim5 0 --mp 6.23564523133908,4.18995661760974 --score-min L,5.18569394284114,4.3845798907286 -f -p 2 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 933s 90 reads; of these: 933s 90 (100.00%) were paired; of these: 933s 89 (98.89%) aligned concordantly 0 times 933s 0 (0.00%) aligned concordantly exactly 1 time 933s 1 (1.11%) aligned concordantly >1 times 933s ---- 933s 89 pairs aligned concordantly 0 times; of these: 933s 0 (0.00%) aligned discordantly 1 time 933s ---- 933s 89 pairs aligned 0 times concordantly or discordantly; of these: 933s 178 mates make up the pairs; of these: 933s 160 (89.89%) aligned 0 times 933s 11 (6.18%) aligned exactly 1 time 933s 7 (3.93%) aligned >1 times 933s 11.11% overall alignment rate 933s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 933s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '4' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 933s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '10' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 933s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '66' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 933s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #1 of read '85' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 933s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (0) 933s Warning: skipping mate #2 of read '72' because it was < 2 characters long 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 933s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 933s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 933s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 933s 90 reads; of these: 933s 90 (100.00%) were paired; of these: 933s 89 (98.89%) aligned concordantly 0 times 933s 0 (0.00%) aligned concordantly exactly 1 time 933s 1 (1.11%) aligned concordantly >1 times 933s ---- 933s 89 pairs aligned concordantly 0 times; of these: 933s 0 (0.00%) aligned discordantly 1 time 933s ---- 933s 89 pairs aligned 0 times concordantly or discordantly; of these: 933s 178 mates make up the pairs; of these: 933s 160 (89.89%) aligned 0 times 933s 11 (6.18%) aligned exactly 1 time 933s 7 (3.93%) aligned >1 times 933s 11.11% overall alignment rate 933s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 933s Flattened IUPAC characters 933s Mutating sequence Sim.pm.2 933s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 933s Finished SNPs 933s Finished ref gaps 933s Finished read gaps 933s Mutating sequence Sim.pm.1 933s Introducing 11 SNPs, 0/1 ref/read gaps, and 0 rearrangements 933s Finished SNPs 933s Finished ref gaps 933s Finished read gaps 933s Mutated reference genome to subject genome 933s SNPs introduced: 18 933s Reference gaps introduced: 0 933s Read gaps introduced: 1 933s Rearrangements introduced: 0 933s Created read sampler 933s Sampling 117 reads 933s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 933s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 933s parsing sequence Sim.pm.1... 933s parsing sequence Sim.pm.2... 933s Parsed 74 reference bases 933s *** Run 92 of 100 933s /usr/bin/bowtie2 --rdg 46.1671427470665,11.1524438527216 --mp 3.61159481526611,2.23924749732764 --trim3 3 -a --ma 31.2751708679784 --cp-min 8 --cp-ival 1 --rfg 24.1843099136214,10.0559295698786 --trim5 9 --score-min L,5.43245940737382,4.56469613406769 --np 3 -D 40 -N 1 -L19 -f -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta 934s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 934s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 934s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '2' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 934s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '6' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 934s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '12' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 934s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '16' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 934s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 934s Warning: skipping read '17' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 934s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '23' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 934s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '24' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 934s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '25' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 934s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 934s Warning: skipping read '38' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 934s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 934s Warning: skipping read '39' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 934s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '47' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 934s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '48' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 934s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '52' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 934s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '59' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 934s Read 50 alignments... 934s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 934s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '68' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 934s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '69' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 934s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 934s Warning: skipping read '77' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 934s Warning: skipping read '79' because length (0) <= # seed mismatches (1) 934s Warning: skipping read '79' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 934s Read 100 alignments... 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 934s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '88' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 934s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '91' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 934s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '93' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 934s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '98' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 934s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (1) 934s Warning: skipping mate #2 of read '99' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 934s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '102' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 934s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '104' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 934s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '105' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 934s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '109' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 934s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '113' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 934s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '117' because it was < 2 characters long 934s 117 reads; of these: 934s 89 (76.07%) were paired; of these: 934s 88 (98.88%) aligned concordantly 0 times 934s 0 (0.00%) aligned concordantly exactly 1 time 934s 1 (1.12%) aligned concordantly >1 times 934s ---- 934s 88 pairs aligned concordantly 0 times; of these: 934s 0 (0.00%) aligned discordantly 1 time 934s ---- 934s 88 pairs aligned 0 times concordantly or discordantly; of these: 934s 176 mates make up the pairs; of these: 934s 153 (86.93%) aligned 0 times 934s 16 (9.09%) aligned exactly 1 time 934s 7 (3.98%) aligned >1 times 934s 28 (23.93%) were unpaired; of these: 934s 27 (96.43%) aligned 0 times 934s 1 (3.57%) aligned exactly 1 time 934s 0 (0.00%) aligned >1 times 934s 12.62% overall alignment rate 934s Read 150 alignments... 934s Read 200 alignments... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s AG 934s AG 934s Processing line... 934s AGAGGCGG 934s AGAGGCGG 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s TACACAAAG 934s TACACAAAG 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s GGT 934s GGT 934s Processing line... 934s ACC 934s ACC 934s Processing line... 934s GGT 934s GGT 934s Processing line... 934s Processing line... 934s ACTCTTTACACAAAGAG 934s ACTCTTTACACAAAGAG 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s ATGAC 934s ATGAC 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s ACATG 934s ACATG 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s TCA 934s TCA 934s Processing line... 934s TGA 934s TGA 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s CTTT 934s CTTT 934s Processing line... 934s AAAG 934s AAAG 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s TACAT 934s TACAT 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s GGAGGGCGATAAGGG 934s GGAGGGCGATAAGGG 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s GGTG 934s GGTG 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s TA 934s TA 934s Processing line... 934s Processing line... 934s CTA 934s CTA 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s GGGG 934s GGGG 934s Processing line... 934s AGG 934s AGG 934s Processing line... 934s AGG 934s AGG 934s Processing line... 934s AGG 934s AGG 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s AAAGAGGCGGG 934s AAAGAGGCGGG 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s CGGGGTAA 934s CGGGGTAA 934s Processing line... 934s Processing line... 934s ACTCTTTACACAAAGAGGCGGGGT 934s ACTCTTTACACAAAGAGGCGGGGT 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s TCTTTAC 934s TCTTTAC 934s Processing line... 934s Processing line... 934s TACATGACTCTTTACA 934s TACATGACTCTTTACA 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s CTTTACACAAAGAGGCGGGG 934s CTTTACACAAAGAGGCGGGG 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s TTA 934s TTA 934s Processing line... 934s TAA 934s TAA 934s Processing line... 934s TAA 934s TAA 934s Processing line... 934s Processing line... 934s AAGAGGCGG 934s AAGAGGCGG 934s Processing line... 934s Processing line... 934s AC 934s AC 934s Processing line... 934s GT 934s GT 934s Processing line... 934s AC 934s AC 934s Processing line... 934s GT 934s GT 934s Processing line... 934s AC 934s AC 934s Processing line... 934s AC 934s AC 934s Processing line... 934s AC 934s AC 934s Processing line... 934s GT 934s GT 934s Processing line... 934s AC 934s AC 934s Processing line... 934s AC 934s AC 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s GAGGC 934s GAGGC 934s Processing line... 934s --- Summary --- 934s Read 1 reference strings 934s Checked 54 alignments, 0 edits 934s --------------- 934s PASSED 934s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 934s /usr/bin/bowtie2 --rdg 46.1671427470665,11.1524438527216 --mp 3.61159481526611,2.23924749732764 --trim3 3 -a --ma 31.2751708679784 --cp-min 8 --cp-ival 1 --rfg 24.1843099136214,10.0559295698786 --trim5 9 --score-min L,5.43245940737382,4.56469613406769 --np 3 -D 40 -N 1 -L19 -f -p 3 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fasta -2 /tmp/Sim.pm.77cQkkTL_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 934s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 934s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 934s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '2' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 934s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 934s Warning: skipping read '17' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 934s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '6' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 934s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '23' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 934s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '12' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 934s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '24' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 934s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '25' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 934s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 934s Warning: skipping read '38' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 934s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 934s Warning: skipping read '39' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 934s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '47' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 934s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '16' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 934s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '52' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 934s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '59' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 934s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '68' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 934s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '69' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 934s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '48' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 934s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '88' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 934s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '98' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 934s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (1) 934s Warning: skipping mate #2 of read '99' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 934s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '102' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 934s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '104' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 934s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '105' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 934s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '109' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 934s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 934s Warning: skipping read '77' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 934s Warning: skipping read '79' because length (0) <= # seed mismatches (1) 934s Warning: skipping read '79' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 934s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (1) 934s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 934s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 934s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 934s *** Run 93 of 100 934s /usr/bin/bowtie2 --cp-min 3 --cp-ival 2 --local --trim3 3 --mp 5.37777867685593,3.95877611241116 -a --nofw --np 6 --norc -i L,0.484757373903122 --rfg 38.2065043503199 --score-min L,7.79724627442934,8.21701694300698 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 934s Warning: skipping mate #1 of read '113' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 934s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '117' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 934s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '91' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 934s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (1) 934s Warning: skipping mate #1 of read '93' because it was < 2 characters long 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 934s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 934s 117 reads; of these: 934s 89 (76.07%) were paired; of these: 934s 88 (98.88%) aligned concordantly 0 times 934s 0 (0.00%) aligned concordantly exactly 1 time 934s 1 (1.12%) aligned concordantly >1 times 934s ---- 934s 88 pairs aligned concordantly 0 times; of these: 934s 0 (0.00%) aligned discordantly 1 time 934s ---- 934s 88 pairs aligned 0 times concordantly or discordantly; of these: 934s 176 mates make up the pairs; of these: 934s 153 (86.93%) aligned 0 times 934s 16 (9.09%) aligned exactly 1 time 934s 7 (3.98%) aligned >1 times 934s 28 (23.93%) were unpaired; of these: 934s 27 (96.43%) aligned 0 times 934s 1 (3.57%) aligned exactly 1 time 934s 0 (0.00%) aligned >1 times 934s 12.62% overall alignment rate 934s Flattened IUPAC characters 934s Mutating sequence Sim.pm.2 934s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 934s Finished SNPs 934s Finished ref gaps 934s Finished read gaps 934s Mutating sequence Sim.pm.1 934s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 934s Finished SNPs 934s Finished ref gaps 934s Finished read gaps 934s Mutated reference genome to subject genome 934s SNPs introduced: 10 934s Reference gaps introduced: 0 934s Read gaps introduced: 2 934s Rearrangements introduced: 0 934s Created read sampler 934s Sampling 38 reads 934s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 934s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 934s parsing sequence Sim.pm.1... 934s parsing sequence Sim.pm.2... 934s Parsed 74 reference bases 934s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 934s Warning: skipping read '3' because it was < 2 characters long 934s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 934s Warning: skipping read '22' because it was < 2 characters long 934s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 934s Warning: skipping read '23' because it was < 2 characters long 934s 38 reads; of these: 934s 38 (100.00%) were unpaired; of these: 934s 38 (100.00%) aligned 0 times 934s 0 (0.00%) aligned exactly 1 time 934s 0 (0.00%) aligned >1 times 934s 0.00% overall alignment rate 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s Processing line... 934s --- Summary --- 934s Read 1 reference strings 934s Checked 0 alignments, 0 edits 934s --------------- 934s PASSED 934s Flattened IUPAC characters 934s Mutating sequence Sim.pm.2 934s Introducing 10 SNPs, 1/0 ref/read gaps, and 1 rearrangements 934s Finished SNPs 934s Finished ref gaps 934s Finished read gaps 934s Mutating sequence Sim.pm.1 934s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 934s Finished SNPs 934s Finished ref gaps 934s Finished read gaps 934s Mutated reference genome to subject genome 934s SNPs introduced: 12 934s Reference gaps introduced: 1 934s Read gaps introduced: 0 934s Rearrangements introduced: 1 934s Created read sampler 934s Sampling 72 reads 934s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.raw & /tmp/Sim.pm.77cQkkTL_2.raw 934s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 934s parsing sequence Sim.pm.1... 934s parsing sequence Sim.pm.2... 934s Parsed 74 reference bases 934s *** Run 94 of 100 934s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 4 --local -a -N 1 -L14 --nofw --np 3 --norc --score-min L,2.31003284005113,3.87197974562565 --n-ceil 0.741116431539365,0.00851396318696759 -i S,1.73637041151127 -r -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.raw 935s Warning: skipping read '49' because length (1) <= # seed mismatches (1) 935s Warning: skipping read '49' because it was < 2 characters long 935s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 935s Warning: skipping read '51' because it was < 2 characters long 935s Warning: skipping read '56' because length (1) <= # seed mismatches (1) 935s Warning: skipping read '56' because it was < 2 characters long 935s 72 reads; of these: 935s 72 (100.00%) were unpaired; of these: 935s 72 (100.00%) aligned 0 times 935s 0 (0.00%) aligned exactly 1 time 935s 0 (0.00%) aligned >1 times 935s 0.00% overall alignment rate 935s Read 50 alignments... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s --- Summary --- 935s Read 1 reference strings 935s Checked 0 alignments, 0 edits 935s --------------- 935s PASSED 935s Flattened IUPAC characters 935s Mutating sequence Sim.pm.1 935s Introducing 6 SNPs, 1/0 ref/read gaps, and 3 rearrangements 935s Finished SNPs 935s Finished ref gaps 935s Finished read gaps 935s Mutating sequence Sim.pm.2 935s Introducing 11 SNPs, 1/0 ref/read gaps, and 0 rearrangements 935s Finished SNPs 935s Finished ref gaps 935s Finished read gaps 935s Mutated reference genome to subject genome 935s SNPs introduced: 17 935s Reference gaps introduced: 2 935s Read gaps introduced: 0 935s Rearrangements introduced: 3 935s Created read sampler 935s Sampling 96 reads 935s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 935s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 935s parsing sequence Sim.pm.1... 935s parsing sequence Sim.pm.2... 935s Parsed 74 reference bases 935s *** Run 95 of 100 935s /usr/bin/bowtie2 --cp-min 4 --mm --cp-ival 1 --rdg 39.9750839112709,3.05470890488953 --mp 8.34178872641737,2.30084221277926 --local --norc --np 1 --nofw -R 3 --n-ceil 1.26775601634721,0.586570200444417 --gbar 1 --score-min L,4.62213583936987,4.31458406883275 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 935s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 935s Warning: skipping mate #2 of read '62' because it was < 2 characters long 935s Read 50 alignments... 935s Read 100 alignments... 935s Warning: skipping mate #1 of read '81' because length (1) <= # seed mismatches (0) 935s Warning: skipping mate #1 of read '81' because it was < 2 characters long 935s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (0) 935s Warning: skipping mate #1 of read '86' because it was < 2 characters long 935s 96 reads; of these: 935s 96 (100.00%) were paired; of these: 935s 96 (100.00%) aligned concordantly 0 times 935s 0 (0.00%) aligned concordantly exactly 1 time 935s 0 (0.00%) aligned concordantly >1 times 935s ---- 935s 96 pairs aligned concordantly 0 times; of these: 935s 0 (0.00%) aligned discordantly 1 time 935s ---- 935s 96 pairs aligned 0 times concordantly or discordantly; of these: 935s 192 mates make up the pairs; of these: 935s 192 (100.00%) aligned 0 times 935s 0 (0.00%) aligned exactly 1 time 935s 0 (0.00%) aligned >1 times 935s 0.00% overall alignment rate 935s Read 150 alignments... 935s Processing line... 935s Processing line... 935s /usr/bin/bowtie2 --cp-min 4 --mm --cp-ival 1 --rdg 39.9750839112709,3.05470890488953 --mp 8.34178872641737,2.30084221277926 --local --norc --np 1 --nofw -R 3 --n-ceil 1.26775601634721,0.586570200444417 --gbar 1 --score-min L,4.62213583936987,4.31458406883275 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s --- Summary --- 935s Read 1 reference strings 935s Checked 0 alignments, 0 edits 935s --------------- 935s PASSED 935s ALSO checking that bowtie2 and bowtie2-align match up 935s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 935s Warning: skipping mate #2 of read '62' because it was < 2 characters long 935s Warning: skipping mate #1 of read '81' because length (1) <= # seed mismatches (0) 935s Warning: skipping mate #1 of read '81' because it was < 2 characters long 935s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (0) 935s Warning: skipping mate #1 of read '86' because it was < 2 characters long 935s 96 reads; of these: 935s 96 (100.00%) were paired; of these: 935s 96 (100.00%) aligned concordantly 0 times 935s 0 (0.00%) aligned concordantly exactly 1 time 935s 0 (0.00%) aligned concordantly >1 times 935s ---- 935s 96 pairs aligned concordantly 0 times; of these: 935s 0 (0.00%) aligned discordantly 1 time 935s ---- 935s 96 pairs aligned 0 times concordantly or discordantly; of these: 935s 192 mates make up the pairs; of these: 935s 192 (100.00%) aligned 0 times 935s 0 (0.00%) aligned exactly 1 time 935s 0 (0.00%) aligned >1 times 935s 0.00% overall alignment rate 935s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 935s Flattened IUPAC characters 935s Mutating sequence Sim.pm.2 935s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 935s Finished SNPs 935s Finished ref gaps 935s Finished read gaps 935s Mutating sequence Sim.pm.1 935s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 935s Finished SNPs 935s Finished ref gaps 935s Finished read gaps 935s Mutated reference genome to subject genome 935s SNPs introduced: 8 935s Reference gaps introduced: 0 935s Read gaps introduced: 0 935s Rearrangements introduced: 1 935s Created read sampler 935s Sampling 101 reads 935s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 935s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 935s parsing sequence Sim.pm.1... 935s parsing sequence Sim.pm.2... 935s Parsed 74 reference bases 935s *** Run 96 of 100 935s /usr/bin/bowtie2 --trim5 2 --mp 6.57916878733288,3.6745427136012 --score-min L,1.83103106479982,9.54257909493485 --np 2 --cp-min 2 --cp-ival 2 -D 32 -N 1 -L24 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 935s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 935s Warning: skipping read '3' because length (1) <= # seed mismatches (1) 935s Warning: skipping read '3' because it was < 2 characters long 935s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 935s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 935s Warning: skipping read '15' because it was < 2 characters long 935s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 935s Warning: skipping read '40' because length (1) <= # seed mismatches (1) 935s Warning: skipping read '40' because it was < 2 characters long 935s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 935s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 935s Warning: skipping read '70' because it was < 2 characters long 935s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 935s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 935s Warning: skipping read '76' because it was < 2 characters long 935s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 935s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 935s Warning: skipping read '77' because it was < 2 characters long 935s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 935s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 935s Warning: skipping read '99' because it was < 2 characters long 935s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 935s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 935s Warning: skipping read '101' because length (0) <= # seed mismatches (1) 935s Warning: skipping read '101' because it was < 2 characters long 935s 101 reads; of these: 935s 101 (100.00%) were unpaired; of these: 935s 83 (82.18%) aligned 0 times 935s 10 (9.90%) aligned exactly 1 time 935s 8 (7.92%) aligned >1 times 935s 17.82% overall alignment rate 935s Read 50 alignments... 935s Read 100 alignments... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s AA 935s AA 935s Processing line... 935s Processing line... 935s /usr/bin/bowtie2 --trim5 2 --mp 6.57916878733288,3.6745427136012 --score-min L,1.83103106479982,9.54257909493485 --np 2 --cp-min 2 --cp-ival 2 -D 32 -N 1 -L24 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.als 935s Processing line... 935s Processing line... 935s Processing line... 935s TCTTTACACAAAGAGGCGGGGTAA 935s TCTTTACACAAAGAGGCGGGGTAA 935s Processing line... 935s GGGGTAA 935s GGGGTAA 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s GAGG 935s GAGG 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s CAAAGAGGCGGG 935s CAAAGAGGCGGG 935s Processing line... 935s Processing line... 935s Processing line... 935s CAGCT 935s CAGCT 935s Processing line... 935s TCTTTACACAAAGAGGCGGGGTAA 935s TCTTTACACAAAGAGGCGGGGTAA 935s Processing line... 935s GGGT 935s GGGT 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s GGCGG 935s GGCGG 935s Processing line... 935s Processing line... 935s GACTC 935s GACTC 935s Processing line... 935s AAG 935s AAG 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s CG 935s CG 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s CTCTTTACACAAAGAGGCGG 935s CTCTTTACACAAAGAGGCGG 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s TCT 935s TCT 935s Processing line... 935s CACAAAGAGGCGGGGT 935s CACAAAGAGGCGGGGT 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s GGGT 935s GGGT 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s ACACAAAGAGGCGGGGTAAC 935s ACACAAAGAGGCGGGGTAAC 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s GTA 935s GTA 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s Processing line... 935s --- Summary --- 935s Read 1 reference strings 935s Checked 18 alignments, 0 edits 935s --------------- 935s PASSED 935s ALSO checking that bowtie2 and bowtie2-align match up 936s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 936s Warning: skipping read '3' because length (1) <= # seed mismatches (1) 936s Warning: skipping read '3' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 936s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '15' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 936s Warning: skipping read '40' because length (1) <= # seed mismatches (1) 936s Warning: skipping read '40' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 936s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '70' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 936s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '76' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 936s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '77' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 936s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '99' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 936s Warning: skipping read '101' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '101' because it was < 2 characters long 936s 101 reads; of these: 936s 101 (100.00%) were unpaired; of these: 936s 83 (82.18%) aligned 0 times 936s 10 (9.90%) aligned exactly 1 time 936s 8 (7.92%) aligned >1 times 936s 17.82% overall alignment rate 936s diff -uw /tmp/Sim.pm.77cQkkTL.als /tmp/Sim.pm.77cQkkTL.debug.als 936s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 936s /usr/bin/bowtie2 --trim5 2 --mp 6.57916878733288,3.6745427136012 --score-min L,1.83103106479982,9.54257909493485 --np 2 --cp-min 2 --cp-ival 2 -D 32 -N 1 -L24 -q -p 3 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 936s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 936s Warning: skipping read '3' because length (1) <= # seed mismatches (1) 936s Warning: skipping read '3' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 936s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '15' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 936s Warning: skipping read '40' because length (1) <= # seed mismatches (1) 936s Warning: skipping read '40' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 936s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '70' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 936s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '76' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 936s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '77' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 936s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '99' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 936s Warning: skipping read '101' because length (0) <= # seed mismatches (1) 936s Warning: skipping read '101' because it was < 2 characters long 936s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 936s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 936s 101 reads; of these: 936s 101 (100.00%) were unpaired; of these: 936s 83 (82.18%) aligned 0 times 936s 10 (9.90%) aligned exactly 1 time 936s 8 (7.92%) aligned >1 times 936s 17.82% overall alignment rate 936s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 936s Flattened IUPAC characters 936s Mutating sequence Sim.pm.2 936s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 936s Finished SNPs 936s Finished ref gaps 936s Finished read gaps 936s Mutating sequence Sim.pm.1 936s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 936s Finished SNPs 936s Finished ref gaps 936s Finished read gaps 936s Mutated reference genome to subject genome 936s SNPs introduced: 4 936s Reference gaps introduced: 0 936s Read gaps introduced: 0 936s Rearrangements introduced: 1 936s Created read sampler 936s Sampling 87 reads 936s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 936s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 936s parsing sequence Sim.pm.1... 936s parsing sequence Sim.pm.2... 936s Parsed 74 reference bases 936s *** Run 97 of 100 936s /usr/bin/bowtie2 --cp-min 4 --cp-ival 2 --mm --mp 7.72684821755723,1.15303323185436 --trim3 8 --rdg 18.6075762480702,1.73113122309845 --local -k 12 --norc -D 15 --rfg 21.415502638704 --score-min L,8.9793080171762,2.38379639462693 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 936s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '3' because it was < 2 characters long 936s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '4' because it was < 2 characters long 936s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '6' because it was < 2 characters long 936s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '7' because it was < 2 characters long 936s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '8' because it was < 2 characters long 936s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 936s Warning: skipping read '10' because it was < 2 characters long 936s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '11' because it was < 2 characters long 936s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 936s Warning: skipping read '17' because it was < 2 characters long 936s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '20' because it was < 2 characters long 936s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 936s Warning: skipping read '23' because it was < 2 characters long 936s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 936s Warning: skipping read '26' because it was < 2 characters long 936s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 936s Warning: skipping read '27' because it was < 2 characters long 936s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '32' because it was < 2 characters long 936s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '40' because it was < 2 characters long 936s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 936s Warning: skipping read '55' because it was < 2 characters long 936s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 936s Read 50 alignments... 936s Warning: skipping mate #1 of read '73' because it was < 2 characters long 936s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '76' because it was < 2 characters long 936s Warning: skipping mate #1 of read '87' because length (1) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '87' because it was < 2 characters long 936s Read 100 alignments... 936s 87 reads; of these: 936s 62 (71.26%) were paired; of these: 936s 62 (100.00%) aligned concordantly 0 times 936s 0 (0.00%) aligned concordantly exactly 1 time 936s 0 (0.00%) aligned concordantly >1 times 936s ---- 936s 62 pairs aligned concordantly 0 times; of these: 936s 0 (0.00%) aligned discordantly 1 time 936s ---- 936s 62 pairs aligned 0 times concordantly or discordantly; of these: 936s 124 mates make up the pairs; of these: 936s 124 (100.00%) aligned 0 times 936s 0 (0.00%) aligned exactly 1 time 936s 0 (0.00%) aligned >1 times 936s 25 (28.74%) were unpaired; of these: 936s 25 (100.00%) aligned 0 times 936s 0 (0.00%) aligned exactly 1 time 936s 0 (0.00%) aligned >1 times 936s 0.00% overall alignment rate 936s Read 150 alignments... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s Processing line... 936s --- Summary --- 936s Read 1 reference strings 936s Checked 0 alignments, 0 edits 936s --------------- 936s PASSED 936s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 936s /usr/bin/bowtie2 --cp-min 4 --cp-ival 2 --mm --mp 7.72684821755723,1.15303323185436 --trim3 8 --rdg 18.6075762480702,1.73113122309845 --local -k 12 --norc -D 15 --rfg 21.415502638704 --score-min L,8.9793080171762,2.38379639462693 -q -p 2 -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 936s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '3' because it was < 2 characters long 936s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '4' because it was < 2 characters long 936s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '6' because it was < 2 characters long 936s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '7' because it was < 2 characters long 936s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '8' because it was < 2 characters long 936s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 936s Warning: skipping read '10' because it was < 2 characters long 936s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '11' because it was < 2 characters long 936s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 936s Warning: skipping read '17' because it was < 2 characters long 936s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '20' because it was < 2 characters long 936s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 936s Warning: skipping read '23' because it was < 2 characters long 936s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 936s Warning: skipping read '26' because it was < 2 characters long 936s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 936s Warning: skipping read '27' because it was < 2 characters long 936s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '32' because it was < 2 characters long 936s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '40' because it was < 2 characters long 936s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 936s Warning: skipping read '55' because it was < 2 characters long 936s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '73' because it was < 2 characters long 936s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '76' because it was < 2 characters long 936s Warning: skipping mate #1 of read '87' because length (1) <= # seed mismatches (0) 936s Warning: skipping mate #1 of read '87' because it was < 2 characters long 936s 87 reads; of these: 936s 62 (71.26%) were paired; of these: 936s 62 (100.00%) aligned concordantly 0 times 936s 0 (0.00%) aligned concordantly exactly 1 time 936s 0 (0.00%) aligned concordantly >1 times 936s ---- 936s 62 pairs aligned concordantly 0 times; of these: 936s 0 (0.00%) aligned discordantly 1 time 936s ---- 936s 62 pairs aligned 0 times concordantly or discordantly; of these: 936s 124 mates make up the pairs; of these: 936s 124 (100.00%) aligned 0 times 936s 0 (0.00%) aligned exactly 1 time 936s 0 (0.00%) aligned >1 times 936s 25 (28.74%) were unpaired; of these: 936s 25 (100.00%) aligned 0 times 936s 0 (0.00%) aligned exactly 1 time 936s 0 (0.00%) aligned >1 times 936s 0.00% overall alignment rate 937s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 937s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 937s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 937s Flattened IUPAC characters 937s Mutating sequence Sim.pm.2 937s Introducing 9 SNPs, 1/0 ref/read gaps, and 0 rearrangements 937s Finished SNPs 937s Finished ref gaps 937s Finished read gaps 937s Mutating sequence Sim.pm.1 937s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 937s Finished SNPs 937s Finished ref gaps 937s Finished read gaps 937s Mutated reference genome to subject genome 937s SNPs introduced: 13 937s Reference gaps introduced: 2 937s Read gaps introduced: 0 937s Rearrangements introduced: 1 937s Created read sampler 937s Sampling 80 reads 937s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 937s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 937s parsing sequence Sim.pm.1... 937s parsing sequence Sim.pm.2... 937s Parsed 74 reference bases 937s *** Run 98 of 100 937s /usr/bin/bowtie2 --rdg 27.1904775836461,8.78312464736663 --trim3 5 --mp 7.00511752648046,1.54607041432335 --cp-ival 1 --cp-min 2 --score-min L,7.87806383782785,7.5492749431582 -i L,0.305497458655054 --rfg 18.6097397486809,6.88013426159109 -D 47 --np 10 -q -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq 937s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 937s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '5' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 937s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '9' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 937s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '19' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 937s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '21' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 937s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '22' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 937s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '23' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 937s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '26' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 937s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '29' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 937s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '46' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 937s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '47' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 937s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '49' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 937s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '54' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 937s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '58' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 937s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '60' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 937s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '66' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 937s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '70' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 937s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '73' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 937s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '75' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 937s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '80' because it was < 2 characters long 937s 80 reads; of these: 937s 80 (100.00%) were unpaired; of these: 937s 74 (92.50%) aligned 0 times 937s 4 (5.00%) aligned exactly 1 time 937s 2 (2.50%) aligned >1 times 937s 7.50% overall alignment rate 937s Read 50 alignments... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s AGCTACC 937s AGCTACC 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s GCG 937s GCG 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s TACACAAAGAGGCGGGGTAAC 937s TACACAAAGAGGCGGGGTAAC 937s Processing line... 937s CCA 937s CCA 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s AGGCGGG 937s AGGCGGG 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s GGG 937s GGG 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s Processing line... 937s --- Summary --- 937s Read 1 reference strings 937s Checked 6 alignments, 0 edits 937s --------------- 937s PASSED 937s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 937s /usr/bin/bowtie2 --rdg 27.1904775836461,8.78312464736663 --trim3 5 --mp 7.00511752648046,1.54607041432335 --cp-ival 1 --cp-min 2 --score-min L,7.87806383782785,7.5492749431582 -i L,0.305497458655054 --rfg 18.6097397486809,6.88013426159109 -D 47 --np 10 -q -p 3 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 937s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 937s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '5' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 937s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '9' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 937s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '19' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 937s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '21' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 937s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '22' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 937s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '23' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 937s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '26' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 937s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '29' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 937s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '46' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 937s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '47' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 937s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '49' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 937s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '54' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 937s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '58' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 937s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '66' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 937s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '70' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 937s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '73' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 937s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '75' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 937s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '60' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 937s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '80' because it was < 2 characters long 937s 80 reads; of these: 937s 80 (100.00%) were unpaired; of these: 937s 74 (92.50%) aligned 0 times 937s 4 (5.00%) aligned exactly 1 time 937s 2 (2.50%) aligned >1 times 937s 7.50% overall alignment rate 937s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 937s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 937s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 937s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 937s /usr/bin/bowtie2 --rdg 27.1904775836461,8.78312464736663 --trim3 5 --mp 7.00511752648046,1.54607041432335 --cp-ival 1 --cp-min 2 --score-min L,7.87806383782785,7.5492749431582 -i L,0.305497458655054 --rfg 18.6097397486809,6.88013426159109 -D 47 --np 10 -q -p 3 -x /tmp/Sim.pm.77cQkkTL --reorder /tmp/Sim.pm.77cQkkTL_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 937s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 937s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '5' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 937s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '9' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 937s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '19' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 937s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '21' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 937s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '22' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 937s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '23' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 937s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '26' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 937s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '29' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 937s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '46' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 937s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '47' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 937s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '49' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 937s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '54' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 937s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '66' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 937s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '58' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 937s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 937s Warning: skipping read '60' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 937s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '70' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 937s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '73' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 937s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '75' because it was < 2 characters long 937s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 937s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 937s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 937s Warning: skipping read '80' because it was < 2 characters long 937s 80 reads; of these: 937s 80 (100.00%) were unpaired; of these: 937s 74 (92.50%) aligned 0 times 937s 4 (5.00%) aligned exactly 1 time 937s 2 (2.50%) aligned >1 times 937s 7.50% overall alignment rate 937s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 937s Flattened IUPAC characters 937s Mutating sequence Sim.pm.2 937s Introducing 16 SNPs, 1/0 ref/read gaps, and 0 rearrangements 937s Finished SNPs 937s Finished ref gaps 937s Finished read gaps 937s Mutating sequence Sim.pm.1 937s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 937s Finished SNPs 937s Finished ref gaps 937s Finished read gaps 937s Mutated reference genome to subject genome 937s SNPs introduced: 25 937s Reference gaps introduced: 1 937s Read gaps introduced: 0 937s Rearrangements introduced: 0 937s Created read sampler 937s Sampling 42 reads 937s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fastq & /tmp/Sim.pm.77cQkkTL_2.fastq 937s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 937s parsing sequence Sim.pm.1... 937s parsing sequence Sim.pm.2... 937s Parsed 74 reference bases 937s *** Run 99 of 100 937s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 2 --score-min L,4.10097738103153,2.75358361846516 --n-ceil 0.705750992283614,0.9219494219244 --rfg 16.6908969724207 --trim5 4 --rdg 47.1773047936479,18.0600641035035 -q -x /tmp/Sim.pm.77cQkkTL -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 938s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 938s Warning: skipping mate #1 of read '14' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 938s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 938s Warning: skipping mate #2 of read '15' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 938s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 938s Warning: skipping mate #1 of read '16' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 938s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 938s Warning: skipping mate #1 of read '21' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 938s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 938s Warning: skipping mate #1 of read '27' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 938s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 938s Warning: skipping mate #1 of read '39' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 938s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 938s Warning: skipping mate #2 of read '42' because it was < 2 characters long 938s 42 reads; of these: 938s 36 (85.71%) were paired; of these: 938s 36 (100.00%) aligned concordantly 0 times 938s 0 (0.00%) aligned concordantly exactly 1 time 938s 0 (0.00%) aligned concordantly >1 times 938s ---- 938s 36 pairs aligned concordantly 0 times; of these: 938s 0 (0.00%) aligned discordantly 1 time 938s ---- 938s 36 pairs aligned 0 times concordantly or discordantly; of these: 938s 72 mates make up the pairs; of these: 938s 65 (90.28%) aligned 0 times 938s 5 (6.94%) aligned exactly 1 time 938s 2 (2.78%) aligned >1 times 938s 6 (14.29%) were unpaired; of these: 938s 6 (100.00%) aligned 0 times 938s 0 (0.00%) aligned exactly 1 time 938s 0 (0.00%) aligned >1 times 938s 8.97% overall alignment rate 938s Read 50 alignments... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s GGGGTAA 938s GGGGTAA 938s Processing line... 938s Processing line... 938s TACACAAAGAGGC 938s TACACAAAGAGGC 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s CAGCT 938s CAGCT 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 2 --score-min L,4.10097738103153,2.75358361846516 --n-ceil 0.705750992283614,0.9219494219244 --rfg 16.6908969724207 --trim5 4 --rdg 47.1773047936479,18.0600641035035 -q -p 2 -x /tmp/Sim.pm.77cQkkTL --reorder -1 /tmp/Sim.pm.77cQkkTL_1.fastq -2 /tmp/Sim.pm.77cQkkTL_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.reord.als 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s GGGGTAACATTC 938s GGGGTAACATTC 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s CTTTACACAAAGAGGC 938s CTTTACACAAAGAGGC 938s Processing line... 938s Processing line... 938s GA 938s GA 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s GGT 938s GGT 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s --- Summary --- 938s Read 1 reference strings 938s Checked 7 alignments, 0 edits 938s --------------- 938s PASSED 938s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 938s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 938s Warning: skipping mate #1 of read '21' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 938s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 938s Warning: skipping mate #1 of read '27' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 938s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 938s Warning: skipping mate #1 of read '14' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 938s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 938s Warning: skipping mate #2 of read '15' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 938s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 938s Warning: skipping mate #1 of read '16' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 938s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 938s Warning: skipping mate #1 of read '39' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 938s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 938s Warning: skipping mate #2 of read '42' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 938s 42 reads; of these: 938s 36 (85.71%) were paired; of these: 938s 36 (100.00%) aligned concordantly 0 times 938s 0 (0.00%) aligned concordantly exactly 1 time 938s 0 (0.00%) aligned concordantly >1 times 938s ---- 938s 36 pairs aligned concordantly 0 times; of these: 938s 0 (0.00%) aligned discordantly 1 time 938s ---- 938s 36 pairs aligned 0 times concordantly or discordantly; of these: 938s 72 mates make up the pairs; of these: 938s 65 (90.28%) aligned 0 times 938s 5 (6.94%) aligned exactly 1 time 938s 2 (2.78%) aligned >1 times 938s 6 (14.29%) were unpaired; of these: 938s 6 (100.00%) aligned 0 times 938s 0 (0.00%) aligned exactly 1 time 938s 0 (0.00%) aligned >1 times 938s 8.97% overall alignment rate 938s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als /tmp/Sim.pm.77cQkkTL.px.reord.als 938s Flattened IUPAC characters 938s Mutating sequence Sim.pm.1 938s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 938s Finished SNPs 938s Finished ref gaps 938s Finished read gaps 938s Mutating sequence Sim.pm.2 938s Introducing 8 SNPs, 0/2 ref/read gaps, and 1 rearrangements 938s Finished SNPs 938s Finished ref gaps 938s Finished read gaps 938s Mutated reference genome to subject genome 938s SNPs introduced: 10 938s Reference gaps introduced: 0 938s Read gaps introduced: 3 938s Rearrangements introduced: 1 938s Created read sampler 938s Sampling 81 reads 938s Dumping reads to temporary files /tmp/Sim.pm.77cQkkTL_1.fasta & /tmp/Sim.pm.77cQkkTL_2.fasta 938s Parsing FASTA file /tmp/Sim.pm.77cQkkTL.fa... 938s parsing sequence Sim.pm.1... 938s *** Run 100 of 100 938s /usr/bin/bowtie2 --mm --cp-ival 1 --norc --np 8 --cp-min 3 --score-min L,2.88818174623672,9.73156528229967 -k 7 --ma 26.6304405506642 --rdg 38.6141270958822 --mp 9.81002063669812,7.80752493144927 -f -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta 938s parsing sequence Sim.pm.2... 938s Parsed 74 reference bases 938s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 938s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 938s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 938s Warning: skipping read '17' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 938s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 938s Warning: skipping read '24' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 938s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 938s Warning: skipping read '34' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 938s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 938s Warning: skipping read '66' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 938s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 938s Warning: skipping read '76' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 938s 81 reads; of these: 938s 81 (100.00%) were unpaired; of these: 938s 74 (91.36%) aligned 0 times 938s 6 (7.41%) aligned exactly 1 time 938s 1 (1.23%) aligned >1 times 938s 8.64% overall alignment rate 938s Read 50 alignments... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s ATTCAGCT 938s ATTCAGCT 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s TG 938s TG 938s Processing line... 938s TG 938s TG 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s TGTACATGACTCTTTACACAAAGAGGCGG 938s TGTACATGACTCTTTACACAAAGAGGCGG 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s GGGCC 938s GGGCC 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s TCA 938s TCA 938s Processing line... 938s GGCGATA 938s GGCGATA 938s Processing line... 938s Processing line... 938s Processing line... 938s ACACAAAGAGGCGGGGTAA 938s ACACAAAGAGGCGGGGTAA 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s Processing line... 938s --- Summary --- 938s Read 1 reference strings 938s Checked 8 alignments, 0 edits 938s --------------- 938s PASSED 938s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 938s /usr/bin/bowtie2 --mm --cp-ival 1 --norc --np 8 --cp-min 3 --score-min L,2.88818174623672,9.73156528229967 -k 7 --ma 26.6304405506642 --rdg 38.6141270958822 --mp 9.81002063669812,7.80752493144927 -f -p 2 -x /tmp/Sim.pm.77cQkkTL /tmp/Sim.pm.77cQkkTL_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als 938s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 938s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 938s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 938s Warning: skipping read '17' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 938s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 938s Warning: skipping read '24' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 938s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 938s Warning: skipping read '34' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 938s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 938s Warning: skipping read '66' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 938s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 938s Warning: skipping read '76' because it was < 2 characters long 938s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 938s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 938s 81 reads; of these: 938s 81 (100.00%) were unpaired; of these: 938s 74 (91.36%) aligned 0 times 938s 6 (7.41%) aligned exactly 1 time 938s 1 (1.23%) aligned >1 times 938s 8.64% overall alignment rate 938s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.px.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.px.als.sorted 938s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.77cQkkTL.debug.als | grep -v '^@PG' > /tmp/Sim.pm.77cQkkTL.debug.als.sorted 938s diff -uw /tmp/Sim.pm.77cQkkTL.debug.als.sorted /tmp/Sim.pm.77cQkkTL.px.als.sorted 938s Created DNA generator 938s N frac: 0.035 938s IUPAC frac: 0.002 938s AT/ACGT frac: 0.428 938s A/AT frac: 0.629 938s C/CG frac: 0.345 938s Generating 2 references 938s Generated reference 'Sim.pm.1' of untrimmed length 122, trimmed length 60 939s Generated reference 'Sim.pm.2' of untrimmed length 249, trimmed length 50 939s Wrote references to /tmp/Sim.pm.5TNUEKCv.fa 939s A: 26 939s C: 27 939s G: 44 939s N: 3 939s T: 10 939s Executing: /usr/bin/bowtie2-build --large-index --threads 1 /tmp/Sim.pm.5TNUEKCv.fa /tmp/Sim.pm.5TNUEKCv 939s *** TEST CASE *** 939s Settings: 939s Output files: "/tmp/Sim.pm.5TNUEKCv.*.bt2l" 939s Line rate: 7 (line is 128 bytes) 939s Lines per side: 1 (side is 128 bytes) 939s Offset rate: 4 (one in 16) 939s FTable chars: 10 939s Strings: unpacked 939s Max bucket size: default 939s Max bucket size, sqrt multiplier: default 939s Max bucket size, len divisor: 4 939s Difference-cover sample period: 1024 939s Endianness: little 939s Actual local endianness: little 939s Sanity checking: disabled 939s Assertions: disabled 939s Random seed: 0 939s Sizeofs: void*:8, int:4, long:8, size_t:8 939s Input files DNA, FASTA: 939s /tmp/Sim.pm.5TNUEKCv.fa 939s Reading reference sizes 939s Time reading reference sizes: 00:00:00 939s Calculating joined length 939s Writing header 939s Reserving space for joined string 939s Joining reference sequences 939s Building a LARGE index 939s Time to join reference sequences: 00:00:00 939s bmax according to bmaxDivN setting: 26 939s Using parameters --bmax 20 --dcv 1024 939s Doing ahead-of-time memory usage test 939s Passed! Constructing with these parameters: --bmax 20 --dcv 1024 939s Constructing suffix-array element generator 939s Building DifferenceCoverSample 939s Building sPrime 939s Building sPrimeOrder 939s V-Sorting samples 939s V-Sorting samples time: 00:00:00 939s Allocating rank array 939s Ranking v-sort output 939s Ranking v-sort output time: 00:00:00 939s Invoking Larsson-Sadakane on ranks 939s Invoking Larsson-Sadakane on ranks time: 00:00:00 939s Sanity-checking and returning 939s Building samples 939s Reserving space for 12 sample suffixes 939s Generating random suffixes 939s QSorting 12 sample offsets, eliminating duplicates 939s QSorting sample offsets, eliminating duplicates time: 00:00:00 939s Multikey QSorting 12 samples 939s (Using difference cover) 939s Multikey QSorting samples time: 00:00:00 939s Calculating bucket sizes 939s Splitting and merging 939s Splitting and merging time: 00:00:00 939s Split 2, merged 7; iterating... 939s Splitting and merging 939s Splitting and merging time: 00:00:00 939s Avg bucket size: 12.5 (target: 19) 939s Converting suffix-array elements to index image 939s Allocating ftab, absorbFtab 939s Entering Ebwt loop 939s Getting block 1 of 8 939s Reserving size (20) for bucket 1 939s Calculating Z arrays for bucket 1 939s Entering block accumulator loop for bucket 1: 939s bucket 1: 10% 939s bucket 1: 20% 939s bucket 1: 30% 939s bucket 1: 40% 939s bucket 1: 50% 939s bucket 1: 60% 939s bucket 1: 70% 939s bucket 1: 80% 939s bucket 1: 90% 939s bucket 1: 100% 939s Sorting block of length 8 for bucket 1 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 9 for bucket 1 939s Getting block 2 of 8 939s Reserving size (20) for bucket 2 939s Calculating Z arrays for bucket 2 939s Entering block accumulator loop for bucket 2: 939s bucket 2: 10% 939s bucket 2: 20% 939s bucket 2: 30% 939s bucket 2: 40% 939s bucket 2: 50% 939s bucket 2: 60% 939s bucket 2: 70% 939s bucket 2: 80% 939s bucket 2: 90% 939s bucket 2: 100% 939s Sorting block of length 13 for bucket 2 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 14 for bucket 2 939s Getting block 3 of 8 939s Reserving size (20) for bucket 3 939s Calculating Z arrays for bucket 3 939s Entering block accumulator loop for bucket 3: 939s bucket 3: 10% 939s bucket 3: 20% 939s bucket 3: 30% 939s bucket 3: 40% 939s bucket 3: 50% 939s bucket 3: 60% 939s bucket 3: 70% 939s bucket 3: 80% 939s bucket 3: 90% 939s bucket 3: 100% 939s Sorting block of length 8 for bucket 3 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 9 for bucket 3 939s Getting block 4 of 8 939s Reserving size (20) for bucket 4 939s Calculating Z arrays for bucket 4 939s Entering block accumulator loop for bucket 4: 939s bucket 4: 10% 939s bucket 4: 20% 939s bucket 4: 30% 939s bucket 4: 40% 939s bucket 4: 50% 939s bucket 4: 60% 939s bucket 4: 70% 939s bucket 4: 80% 939s bucket 4: 90% 939s bucket 4: 100% 939s Sorting block of length 14 for bucket 4 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 15 for bucket 4 939s Getting block 5 of 8 939s Reserving size (20) for bucket 5 939s Calculating Z arrays for bucket 5 939s Entering block accumulator loop for bucket 5: 939s bucket 5: 10% 939s bucket 5: 20% 939s bucket 5: 30% 939s bucket 5: 40% 939s bucket 5: 50% 939s bucket 5: 60% 939s bucket 5: 70% 939s bucket 5: 80% 939s bucket 5: 90% 939s bucket 5: 100% 939s Sorting block of length 19 for bucket 5 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 20 for bucket 5 939s Getting block 6 of 8 939s Reserving size (20) for bucket 6 939s Calculating Z arrays for bucket 6 939s Entering block accumulator loop for bucket 6: 939s bucket 6: 10% 939s bucket 6: 20% 939s bucket 6: 30% 939s bucket 6: 40% 939s bucket 6: 50% 939s bucket 6: 60% 939s bucket 6: 70% 939s bucket 6: 80% 939s bucket 6: 90% 939s bucket 6: 100% 939s Sorting block of length 13 for bucket 6 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 14 for bucket 6 939s Getting block 7 of 8 939s Reserving size (20) for bucket 7 939s Calculating Z arrays for bucket 7 939s Entering block accumulator loop for bucket 7: 939s bucket 7: 10% 939s bucket 7: 20% 939s bucket 7: 30% 939s bucket 7: 40% 939s bucket 7: 50% 939s bucket 7: 60% 939s bucket 7: 70% 939s bucket 7: 80% 939s bucket 7: 90% 939s bucket 7: 100% 939s Sorting block of length 19 for bucket 7 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 20 for bucket 7 939s Getting block 8 of 8 939s Reserving size (20) for bucket 8 939s Calculating Z arrays for bucket 8 939s Entering block accumulator loop for bucket 8: 939s bucket 8: 10% 939s bucket 8: 20% 939s bucket 8: 30% 939s bucket 8: 40% 939s bucket 8: 50% 939s bucket 8: 60% 939s bucket 8: 70% 939s bucket 8: 80% 939s bucket 8: 90% 939s bucket 8: 100% 939s Sorting block of length 6 for bucket 8 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 7 for bucket 8 939s Exited Ebwt loop 939s fchr[A]: 0 939s fchr[C]: 26 939s fchr[G]: 53 939s fchr[T]: 97 939s fchr[$]: 107 939s Exiting Ebwt::buildToDisk() 939s Returning from initFromVector 939s Wrote 8389155 bytes to primary EBWT file: /tmp/Sim.pm.5TNUEKCv.1.bt2l.tmp 939s Wrote 60 bytes to secondary EBWT file: /tmp/Sim.pm.5TNUEKCv.2.bt2l.tmp 939s Re-opening _in1 and _in2 as input streams 939s Returning from Ebwt constructor 939s Headers: 939s len: 107 939s bwtLen: 108 939s sz: 27 939s bwtSz: 27 939s lineRate: 7 939s offRate: 4 939s offMask: 0xfffffffffffffff0 939s ftabChars: 10 939s eftabLen: 20 939s eftabSz: 160 939s ftabLen: 1048577 939s ftabSz: 8388616 939s offsLen: 7 939s offsSz: 56 939s lineSz: 128 939s sideSz: 128 939s sideBwtSz: 96 939s sideBwtLen: 384 939s numSides: 1 939s numLines: 1 939s ebwtTotLen: 128 939s ebwtTotSz: 128 939s color: 0 939s reverse: 0 939s Total time for call to driver() for forward index: 00:00:00 939s Reading reference sizes 939s Time reading reference sizes: 00:00:00 939s Calculating joined length 939s Writing header 939s Reserving space for joined string 939s Joining reference sequences 939s Time to join reference sequences: 00:00:00 939s Time to reverse reference sequence: 00:00:00 939s bmax according to bmaxDivN setting: 26 939s Using parameters --bmax 20 --dcv 1024 939s Doing ahead-of-time memory usage test 939s Passed! Constructing with these parameters: --bmax 20 --dcv 1024 939s Constructing suffix-array element generator 939s Building DifferenceCoverSample 939s Building sPrime 939s Building sPrimeOrder 939s V-Sorting samples 939s V-Sorting samples time: 00:00:00 939s Allocating rank array 939s Ranking v-sort output 939s Ranking v-sort output time: 00:00:00 939s Invoking Larsson-Sadakane on ranks 939s Invoking Larsson-Sadakane on ranks time: 00:00:00 939s Sanity-checking and returning 939s Building samples 939s Reserving space for 12 sample suffixes 939s Generating random suffixes 939s QSorting 12 sample offsets, eliminating duplicates 939s QSorting sample offsets, eliminating duplicates time: 00:00:00 939s Multikey QSorting 12 samples 939s (Using difference cover) 939s Multikey QSorting samples time: 00:00:00 939s Calculating bucket sizes 939s Splitting and merging 939s Splitting and merging time: 00:00:00 939s Split 1, merged 5; iterating... 939s Splitting and merging 939s Splitting and merging time: 00:00:00 939s Avg bucket size: 12.5 (target: 19) 939s Converting suffix-array elements to index image 939s Allocating ftab, absorbFtab 939s Entering Ebwt loop 939s Getting block 1 of 8 939s Reserving size (20) for bucket 1 939s Calculating Z arrays for bucket 1 939s Entering block accumulator loop for bucket 1: 939s bucket 1: 10% 939s bucket 1: 20% 939s bucket 1: 30% 939s bucket 1: 40% 939s bucket 1: 50% 939s bucket 1: 60% 939s bucket 1: 70% 939s bucket 1: 80% 939s bucket 1: 90% 939s bucket 1: 100% 939s Sorting block of length 3 for bucket 1 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 4 for bucket 1 939s Getting block 2 of 8 939s Reserving size (20) for bucket 2 939s Calculating Z arrays for bucket 2 939s Entering block accumulator loop for bucket 2: 939s bucket 2: 10% 939s bucket 2: 20% 939s bucket 2: 30% 939s bucket 2: 40% 939s bucket 2: 50% 939s bucket 2: 60% 939s bucket 2: 70% 939s bucket 2: 80% 939s bucket 2: 90% 939s bucket 2: 100% 939s Sorting block of length 17 for bucket 2 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 18 for bucket 2 939s Getting block 3 of 8 939s Reserving size (20) for bucket 3 939s Calculating Z arrays for bucket 3 939s Entering block accumulator loop for bucket 3: 939s bucket 3: 10% 939s bucket 3: 20% 939s bucket 3: 30% 939s bucket 3: 40% 939s bucket 3: 50% 939s bucket 3: 60% 939s bucket 3: 70% 939s bucket 3: 80% 939s bucket 3: 90% 939s bucket 3: 100% 939s Sorting block of length 17 for bucket 3 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 18 for bucket 3 939s Getting block 4 of 8 939s Reserving size (20) for bucket 4 939s Calculating Z arrays for bucket 4 939s Entering block accumulator loop for bucket 4: 939s bucket 4: 10% 939s bucket 4: 20% 939s bucket 4: 30% 939s bucket 4: 40% 939s bucket 4: 50% 939s bucket 4: 60% 939s bucket 4: 70% 939s bucket 4: 80% 939s bucket 4: 90% 939s bucket 4: 100% 939s Sorting block of length 14 for bucket 4 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 15 for bucket 4 939s Getting block 5 of 8 939s Reserving size (20) for bucket 5 939s Calculating Z arrays for bucket 5 939s Entering block accumulator loop for bucket 5: 939s bucket 5: 10% 939s bucket 5: 20% 939s bucket 5: 30% 939s bucket 5: 40% 939s bucket 5: 50% 939s bucket 5: 60% 939s bucket 5: 70% 939s bucket 5: 80% 939s bucket 5: 90% 939s bucket 5: 100% 939s Sorting block of length 7 for bucket 5 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 8 for bucket 5 939s Getting block 6 of 8 939s Reserving size (20) for bucket 6 939s Calculating Z arrays for bucket 6 939s Entering block accumulator loop for bucket 6: 939s bucket 6: 10% 939s bucket 6: 20% 939s bucket 6: 30% 939s bucket 6: 40% 939s bucket 6: 50% 939s bucket 6: 60% 939s bucket 6: 70% 939s bucket 6: 80% 939s bucket 6: 90% 939s bucket 6: 100% 939s Sorting block of length 19 for bucket 6 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 20 for bucket 6 939s Getting block 7 of 8 939s Reserving size (20) for bucket 7 939s Calculating Z arrays for bucket 7 939s Entering block accumulator loop for bucket 7: 939s bucket 7: 10% 939s bucket 7: 20% 939s bucket 7: 30% 939s bucket 7: 40% 939s bucket 7: 50% 939s bucket 7: 60% 939s bucket 7: 70% 939s bucket 7: 80% 939s bucket 7: 90% 939s bucket 7: 100% 939s Sorting block of length 18 for bucket 7 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 19 for bucket 7 939s Getting block 8 of 8 939s Reserving size (20) for bucket 8 939s Calculating Z arrays for bucket 8 939s Entering block accumulator loop for bucket 8: 939s bucket 8: 10% 939s bucket 8: 20% 939s bucket 8: 30% 939s bucket 8: 40% 939s bucket 8: 50% 939s bucket 8: 60% 939s bucket 8: 70% 939s bucket 8: 80% 939s bucket 8: 90% 939s bucket 8: 100% 939s Sorting block of length 5 for bucket 8 939s (Using difference cover) 939s Sorting block time: 00:00:00 939s Returning block of 6 for bucket 8 939s Exited Ebwt loop 939s fchr[A]: 0 939s fchr[C]: 26 939s fchr[G]: 53 939s fchr[T]: 97 939s fchr[$]: 107 939s Exiting Ebwt::buildToDisk() 939s Returning from initFromVector 939s Wrote 8389155 bytes to primary EBWT file: /tmp/Sim.pm.5TNUEKCv.rev.1.bt2l.tmp 939s Wrote 60 bytes to secondary EBWT file: /tmp/Sim.pm.5TNUEKCv.rev.2.bt2l.tmp 939s Re-opening _in1 and _in2 as input streams 939s Renaming Returning from Ebwt constructor 939s Headers: 939s len: 107 939s bwtLen: 108 939s sz: 27 939s bwtSz: 27 939s lineRate: 7 939s offRate: 4 939s offMask: 0xfffffffffffffff0 939s ftabChars: 10 939s eftabLen: 20 939s eftabSz: 160 939s ftabLen: 1048577 939s ftabSz: 8388616 939s offsLen: 7 939s offsSz: 56 939s lineSz: 128 939s sideSz: 128 939s sideBwtSz: 96 939s sideBwtLen: 384 939s numSides: 1 939s numLines: 1 939s ebwtTotLen: 128 939s ebwtTotSz: 128 939s color: 0 939s reverse: 1 939s Total time for backward call to driver() for mirror index: 00:00:00 939s /tmp/Sim.pm.5TNUEKCv.3.bt2l.tmp to /tmp/Sim.pm.5TNUEKCv.3.bt2l 939s Renaming /tmp/Sim.pm.5TNUEKCv.4.bt2l.tmp to /tmp/Sim.pm.5TNUEKCv.4.bt2l 939s Renaming /tmp/Sim.pm.5TNUEKCv.1.bt2l.tmp to /tmp/Sim.pm.5TNUEKCv.1.bt2l 939s Renaming /tmp/Sim.pm.5TNUEKCv.2.bt2l.tmp to /tmp/Sim.pm.5TNUEKCv.2.bt2l 939s Renaming /tmp/Sim.pm.5TNUEKCv.rev.1.bt2l.tmp to /tmp/Sim.pm.5TNUEKCv.rev.1.bt2l 939s Renaming /tmp/Sim.pm.5TNUEKCv.rev.2.bt2l.tmp to /tmp/Sim.pm.5TNUEKCv.rev.2.bt2l 939s Built nucleotide index '/tmp/Sim.pm.5TNUEKCv' 939s Flattened IUPAC characters 939s Mutating sequence Sim.pm.1 939s Introducing 9 SNPs, 0/0 ref/read gaps, and 2 rearrangements 939s Finished SNPs 939s Finished ref gaps 939s Finished read gaps 939s Mutating sequence Sim.pm.2 939s Introducing 7 SNPs, 1/0 ref/read gaps, and 3 rearrangements 939s Finished SNPs 939s Finished ref gaps 939s Finished read gaps 939s Mutated reference genome to subject genome 939s SNPs introduced: 16 939s Reference gaps introduced: 1 939s Read gaps introduced: 0 939s Rearrangements introduced: 5 939s Created read sampler 939s Sampling 39 reads 939s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 939s *** Run 1 of 100 939s /usr/bin/bowtie2 --cp-ival 2 --cp-min 3 --nofw --ma 30.753194523054 --large-index --score-min L,1.70813484964495,2.920740148175 -a -r -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw 939s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 939s parsing sequence Sim.pm.1... 939s parsing sequence Sim.pm.2... 939s Parsed 110 reference bases 940s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 940s 39 reads; of these: 940s 39 (100.00%) were paired; of these: 940s 39 (100.00%) aligned concordantly 0 times 940s 0 (0.00%) aligned concordantly exactly 1 time 940s 0 (0.00%) aligned concordantly >1 times 940s ---- 940s 39 pairs aligned concordantly 0 times; of these: 940s 0 (0.00%) aligned discordantly 1 time 940s ---- 940s 39 pairs aligned 0 times concordantly or discordantly; of these: 940s 78 mates make up the pairs; of these: 940s 71 (91.03%) aligned 0 times 940s 3 (3.85%) aligned exactly 1 time 940s 4 (5.13%) aligned >1 times 940s 8.97% overall alignment rate 940s Read 50 alignments... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s AAGGGCCTCGCAGCGG 940s AAGGGCCTCGCAGCGG 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s AC 940s AC 940s Processing line... 940s AC 940s AC 940s Processing line... 940s AC 940s AC 940s Processing line... 940s AC 940s AC 940s Processing line... 940s AC 940s AC 940s Processing line... 940s Processing line... 940s AT 940s AT 940s Processing line... 940s AT 940s AT 940s Processing line... 940s AT 940s AT 940s Processing line... 940s AT 940s AT 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s GACAGGGGA 940s GACAGGGGA 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s GGGACAGGGG 940s GGGACAGGGG 940s Processing line... 940s Processing line... 940s GGA 940s GGA 940s Processing line... 940s GGA 940s GGA 940s Processing line... 940s GGA 940s GGA 940s Processing line... 940s GGA 940s GGA 940s Processing line... 940s GGA 940s GGA 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s TC 940s TC 940s Processing line... 940s TC 940s TC 940s Processing line... 940s TC 940s TC 940s Processing line... 940s TC 940s TC 940s Processing line... 940s Processing line... 940s Processing line... 940s --- Summary --- 940s Read 1 reference strings 940s Checked 21 alignments, 0 edits 940s --------------- 940s PASSED 940s Flattened IUPAC characters 940s Mutating sequence Sim.pm.2 940s Introducing 3 SNPs, 2/0 ref/read gaps, and 0 rearrangements 940s Finished SNPs 940s Finished ref gaps 940s Finished read gaps 940s Mutating sequence Sim.pm.1 940s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 940s Finished SNPs 940s Finished ref gaps 940s Finished read gaps 940s Mutated reference genome to subject genome 940s SNPs introduced: 9 940s Reference gaps introduced: 2 940s Read gaps introduced: 0 940s Rearrangements introduced: 0 940s *** Run 2 of 100 940s /usr/bin/bowtie2 --gbar 3 --score-min L,2.84468348082066,6.18523353419493 --rfg 44.0757151737045,11.1146053926747 --trim5 4 -R 3 -D 27 --large-index --local -a --trim3 2 --cp-ival 1 --cp-min 2 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 940s Created read sampler 940s Sampling 29 reads 940s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 940s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 940s parsing sequence Sim.pm.1... 940s parsing sequence Sim.pm.2... 940s Parsed 110 reference bases 940s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 940s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 940s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 940s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 940s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 940s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 940s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 940s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 940s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 940s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 940s 29 reads; of these: 940s 29 (100.00%) were unpaired; of these: 940s 29 (100.00%) aligned 0 times 940s 0 (0.00%) aligned exactly 1 time 940s 0 (0.00%) aligned >1 times 940s 0.00% overall alignment rate 940s Processing line... 940s Processing line... 940s /usr/bin/bowtie2 --gbar 3 --score-min L,2.84468348082066,6.18523353419493 --rfg 44.0757151737045,11.1146053926747 --trim5 4 -R 3 -D 27 --large-index --local -a --trim3 2 --cp-ival 1 --cp-min 2 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s Processing line... 940s --- Summary --- 940s Read 1 reference strings 940s Checked 0 alignments, 0 edits 940s --------------- 940s PASSED 940s ALSO checking that bowtie2 and bowtie2-align match up 940s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 940s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 940s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 940s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 940s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 940s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 940s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 940s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 940s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 940s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 940s 29 reads; of these: 940s 29 (100.00%) were unpaired; of these: 940s 29 (100.00%) aligned 0 times 940s 0 (0.00%) aligned exactly 1 time 940s 0 (0.00%) aligned >1 times 940s 0.00% overall alignment rate 940s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 940s Flattened IUPAC characters 940s Mutating sequence Sim.pm.2 940s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 940s Finished SNPs 940s Finished ref gaps 940s Finished read gaps 940s Mutating sequence Sim.pm.1 940s Introducing 7 SNPs, 0/0 ref/read gaps, and 2 rearrangements 940s Finished SNPs 940s Finished ref gaps 940s Finished read gaps 940s Mutated reference genome to subject genome 940s SNPs introduced: 9 940s Reference gaps introduced: 0 940s Read gaps introduced: 0 940s Rearrangements introduced: 2 940s Created read sampler 940s Sampling 63 reads 940s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 940s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 940s parsing sequence Sim.pm.1... 940s parsing sequence Sim.pm.2... 940s Parsed 110 reference bases 940s *** Run 3 of 100 940s /usr/bin/bowtie2 -D 28 --np 1 --nofw --score-min L,4.97113687291119,2.99039046800844 --rfg 45.9197417130592,4.41763648507143 --cp-ival 2 --mm --cp-min 2 --large-index --ma 34.7329686429828 -k 2 -f -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta 940s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 940s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 940s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 940s Warning: skipping read '6' because it was < 2 characters long 940s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 940s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 940s 63 reads; of these: 941s *** Run 4 of 100 941s /usr/bin/bowtie2 --mp 8.65249878562167,5.12475872393907 -a --trim5 2 --rfg 40.764918526643,13.4196117909937 --local --large-index --score-min L,5.89237518182578,8.62901200049837 --cp-min 2 --np 3 -N 0 -L20 --cp-ival 3 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 941s 63 (100.00%) were unpaired; of these: 941s 52 (82.54%) aligned 0 times 941s 6 (9.52%) aligned exactly 1 time 941s 5 (7.94%) aligned >1 times 941s 17.46% overall alignment rate 941s Read 50 alignments... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s GCGAAC 941s GCGAAC 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s GCAGCG 941s GCAGCG 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s CGAATGCAGATGGGACA 941s CGAATGCAGATGGGACA 941s Processing line... 941s CAGCGGAAGC 941s CAGCGGAAGC 941s Processing line... 941s ACAGGGGA 941s ACAGGGGA 941s Processing line... 941s Processing line... 941s Processing line... 941s ACAAAGGGCC 941s ACAAAGGGCC 941s Processing line... 941s AG 941s AG 941s Processing line... 941s AG 941s AG 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s AG 941s AG 941s Processing line... 941s AG 941s AG 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s CT 941s CT 941s Processing line... 941s CT 941s CT 941s Processing line... 941s CA 941s CA 941s Processing line... 941s CA 941s CA 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s AG 941s AG 941s Processing line... 941s AG 941s AG 941s --- Summary --- 941s Read 1 reference strings 941s Checked 16 alignments, 0 edits 941s --------------- 941s PASSED 941s Flattened IUPAC characters 941s Mutating sequence Sim.pm.2 941s Introducing 7 SNPs, 1/1 ref/read gaps, and 0 rearrangements 941s Finished SNPs 941s Finished ref gaps 941s Finished read gaps 941s Mutating sequence Sim.pm.1 941s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 941s Finished SNPs 941s Finished ref gaps 941s Finished read gaps 941s Mutated reference genome to subject genome 941s SNPs introduced: 10 941s Reference gaps introduced: 2 941s Read gaps introduced: 1 941s Rearrangements introduced: 0 941s Created read sampler 941s Sampling 110 reads 941s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 941s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 941s parsing sequence Sim.pm.1... 941s parsing sequence Sim.pm.2... 941s Parsed 110 reference bases 941s Warning: skipping mate #2 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 941s Read 50 alignments... 941s Read 100 alignments... 941s Read 150 alignments... 941s 110 reads; of these: 941s 108 (98.18%) were paired; of these: 941s 108 (100.00%) aligned concordantly 0 times 941s 0 (0.00%) aligned concordantly exactly 1 time 941s 0 (0.00%) aligned concordantly >1 times 941s ---- 941s 108 pairs aligned concordantly 0 times; of these: 941s 0 (0.00%) aligned discordantly 1 time 941s ---- 941s 108 pairs aligned 0 times concordantly or discordantly; of these: 941s 216 mates make up the pairs; of these: 941s 216 (100.00%) aligned 0 times 941s 0 (0.00%) aligned exactly 1 time 941s 0 (0.00%) aligned >1 times 941s 2 (1.82%) were unpaired; of these: 941s 2 (100.00%) aligned 0 times 941s 0 (0.00%) aligned exactly 1 time 941s 0 (0.00%) aligned >1 times 941s 0.00% overall alignment rate 941s Read 200 alignments... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s /usr/bin/bowtie2 --mp 8.65249878562167,5.12475872393907 -a --trim5 2 --rfg 40.764918526643,13.4196117909937 --local --large-index --score-min L,5.89237518182578,8.62901200049837 --cp-min 2 --np 3 -N 0 -L20 --cp-ival 3 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s 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Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s Processing line... 941s --- Summary --- 941s Read 1 reference strings 941s Checked 0 alignments, 0 edits 941s --------------- 941s PASSED 941s ALSO checking that bowtie2 and bowtie2-align match up 941s Warning: skipping mate #2 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 941s 110 reads; of these: 941s 108 (98.18%) were paired; of these: 941s 108 (100.00%) aligned concordantly 0 times 941s 0 (0.00%) aligned concordantly exactly 1 time 941s 0 (0.00%) aligned concordantly >1 times 941s ---- 941s 108 pairs aligned concordantly 0 times; of these: 941s 0 (0.00%) aligned discordantly 1 time 941s ---- 941s 108 pairs aligned 0 times concordantly or discordantly; of these: 941s 216 mates make up the pairs; of these: 941s 216 (100.00%) aligned 0 times 941s 0 (0.00%) aligned exactly 1 time 941s 0 (0.00%) aligned >1 times 941s 2 (1.82%) were unpaired; of these: 941s 2 (100.00%) aligned 0 times 941s 0 (0.00%) aligned exactly 1 time 941s 0 (0.00%) aligned >1 times 941s 0.00% overall alignment rate 941s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 941s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 941s /usr/bin/bowtie2 --mp 8.65249878562167,5.12475872393907 -a --trim5 2 --rfg 40.764918526643,13.4196117909937 --local --large-index --score-min L,5.89237518182578,8.62901200049837 --cp-min 2 --np 3 -N 0 -L20 --cp-ival 3 --qseq -p 2 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 941s Warning: skipping mate #2 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 941s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 941s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 941s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 941s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 941s 110 reads; of these: 941s 108 (98.18%) were paired; of these: 941s 108 (100.00%) aligned concordantly 0 times 941s 0 (0.00%) aligned concordantly exactly 1 time 941s 0 (0.00%) aligned concordantly >1 times 941s ---- 941s 108 pairs aligned concordantly 0 times; of these: 941s 0 (0.00%) aligned discordantly 1 time 941s ---- 941s 108 pairs aligned 0 times concordantly or discordantly; of these: 941s 216 mates make up the pairs; of these: 941s 216 (100.00%) aligned 0 times 941s 0 (0.00%) aligned exactly 1 time 941s 0 (0.00%) aligned >1 times 941s 2 (1.82%) were unpaired; of these: 941s 2 (100.00%) aligned 0 times 941s 0 (0.00%) aligned exactly 1 time 941s 0 (0.00%) aligned >1 times 941s 0.00% overall alignment rate 941s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 941s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 941s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 941s Flattened IUPAC characters 941s Mutating sequence Sim.pm.2 941s Introducing 11 SNPs, 0/2 ref/read gaps, and 0 rearrangements 941s Finished SNPs 941s Finished ref gaps 941s Finished read gaps 941s Mutating sequence Sim.pm.1 941s Introducing 6 SNPs, 0/4 ref/read gaps, and 1 rearrangements 941s Finished SNPs 941s Finished ref gaps 941s Finished read gaps 941s Mutated reference genome to subject genome 941s SNPs introduced: 17 941s Reference gaps introduced: 0 941s Read gaps introduced: 6 941s Rearrangements introduced: 1 941s Created read sampler 941s Sampling 63 reads 941s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 941s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 941s parsing sequence Sim.pm.1... 941s parsing sequence Sim.pm.2... 941s Parsed 110 reference bases 941s *** Run 5 of 100 941s /usr/bin/bowtie2 -R 1 -N 1 --nofw --score-min L,5.69544617278172,8.42805903655711 --rfg 15.4283633713661,10.181131061351 --trim5 6 --cp-ival 1 --cp-min 4 --large-index --ma 16.2723151841884 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 942s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (1) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Read 50 alignments... 942s 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 942s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (1) 942s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #2 of read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (1) 942s Warning: skipping mate #2 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (1) 942s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 63 reads; of these: 942s 56 (88.89%) were paired; of these: 942s 56 (100.00%) aligned concordantly 0 times 942s 0 (0.00%) aligned concordantly exactly 1 time 942s 0 (0.00%) aligned concordantly >1 times 942s ---- 942s 56 pairs aligned concordantly 0 times; of these: 942s 0 (0.00%) aligned discordantly 1 time 942s ---- 942s 56 pairs aligned 0 times concordantly or discordantly; of these: 942s 112 mates make up the pairs; of these: 942s 102 (91.07%) aligned 0 times 942s 9 (8.04%) aligned exactly 1 time 942s 1 (0.89%) aligned >1 times 942s 7 (11.11%) were unpaired; of these: 942s 7 (100.00%) aligned 0 times 942s 0 (0.00%) aligned exactly 1 time 942s 0 (0.00%) aligned >1 times 942s 8.40% overall alignment rate 942s Read 100 alignments... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s GA 942s GA 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s GACAGGGGAG 942s GACAGGGGAG 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s AAT 942s AAT 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s GGGAGG 942s GGGAGG 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s GCGAACAAAGGGCCTCGC 942s GCGAACAAAGGGCCTCGC 942s Processing line... 942s Processing line... 942s CGAATG 942s CGAATG 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s AAGC 942s AAGC 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s CAGGGGAGGCGAACAAAGGGCCTC 942s CAGGGGAGGCGAACAAAGGGCCTC 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s AATGCAGATGGGA 942s AATGCAGATGGGA 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s GGAGGCG 942s GGAGGCG 942s Processing line... 942s --- Summary --- 942s Read 1 reference strings 942s Checked 10 alignments, 0 edits 942s --------------- 942s PASSED 942s Flattened IUPAC characters 942s Mutating sequence Sim.pm.2 942s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 942s Finished SNPs 942s Finished ref gaps 942s *** Run 6 of 100 942s /usr/bin/bowtie2 --score-min L,1.76799819072701,9.57713274194686 --gbar 2 --trim5 6 -N 1 -L31 --norc -k 2 --large-index --ma 27.2279845096072 --trim3 7 --rdg 12.0380300000462,17.2643438258531 --cp-ival 1 --cp-min 3 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 942s Finished read gaps 942s Mutating sequence Sim.pm.1 942s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 942s Finished SNPs 942s Finished ref gaps 942s Finished read gaps 942s Mutated reference genome to subject genome 942s SNPs introduced: 5 942s Reference gaps introduced: 1 942s Read gaps introduced: 2 942s Rearrangements introduced: 1 942s Created read sampler 942s Sampling 59 reads 942s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 942s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 942s parsing sequence Sim.pm.1... 942s parsing sequence Sim.pm.2... 942s Parsed 110 reference bases 942s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 942s 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 942s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 942s 59 reads; of these: 942s 47 (79.66%) were paired; of these: 942s 47 (100.00%) aligned concordantly 0 times 942s 0 (0.00%) aligned concordantly exactly 1 time 942s 0 (0.00%) aligned concordantly >1 times 942s ---- 942s 47 pairs aligned concordantly 0 times; of these: 942s 0 (0.00%) aligned discordantly 1 time 942s ---- 942s 47 pairs aligned 0 times concordantly or discordantly; of these: 942s 94 mates make up the pairs; of these: 942s 83 (88.30%) aligned 0 times 942s 8 (8.51%) aligned exactly 1 time 942s 3 (3.19%) aligned >1 times 942s 12 (20.34%) were unpaired; of these: 942s 12 (100.00%) aligned 0 times 942s 0 (0.00%) aligned exactly 1 time 942s 0 (0.00%) aligned >1 times 942s 10.38% overall alignment rate 942s Read 50 alignments... 942s Read 100 alignments... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s AT 942s AT 942s Processing line... 942s AT 942s AT 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s AGCGGAAG 942s AGCGGAAG 942s Processing line... 942s Processing line... 942s CGAATGCAG 942s CGAATGCAG 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s AGGGGAGGCGAACAAAGGGCC 942s AGGGGAGGCGAACAAAGGGCC 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s CGC 942s CGC 942s Processing line... 942s CGC 942s CGC 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s ATG 942s ATG 942s Processing line... 942s ATG 942s ATG 942s Processing line... 942s Processing line... 942s Processing line... 942s GCGACCGCGT 942s GCGACCGCGT 942s Processing line... 942s Processing line... 942s AATGCA 942s AATGCA 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s GAATGCAGATGGGACAGGGGAGGCGAACAA 942s GAATGCAGATGGGACAGGGGAGGCGAACAA 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s ACAGCATAGTGCGACCGCG 942s ACAGCATAGTGCGACCGCG 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s Processing line... 942s GCAGA 942s GCAGA 942s Processing line... 942s --- Summary --- 942s Read 1 reference strings 942s Checked 14 alignments, 0 edits 942s --------------- 942s PASSED 942s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 942s /usr/bin/bowtie2 --score-min L,1.76799819072701,9.57713274194686 --gbar 2 --trim5 6 -N 1 -L31 --norc -k 2 --large-index --ma 27.2279845096072 --trim3 7 --rdg 12.0380300000462,17.2643438258531 --cp-ival 1 --cp-min 3 --qseq -p 2 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 942s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 942s 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 942s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s 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 942s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (1) 942s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 942s 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 942s 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 942s 59 reads; of these: 942s 47 (79.66%) were paired; of these: 942s 47 (100.00%) aligned concordantly 0 times 942s 0 (0.00%) aligned concordantly exactly 1 time 942s 0 (0.00%) aligned concordantly >1 times 942s ---- 942s 47 pairs aligned concordantly 0 times; of these: 942s 0 (0.00%) aligned discordantly 1 time 942s ---- 942s 47 pairs aligned 0 times concordantly or discordantly; of these: 942s 94 mates make up the pairs; of these: 942s 83 (88.30%) aligned 0 times 942s 8 (8.51%) aligned exactly 1 time 942s 3 (3.19%) aligned >1 times 942s 12 (20.34%) were unpaired; of these: 942s 12 (100.00%) aligned 0 times 942s 0 (0.00%) aligned exactly 1 time 942s 0 (0.00%) aligned >1 times 942s 10.38% overall alignment rate 942s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 942s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 942s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 942s Flattened IUPAC characters 942s Mutating sequence Sim.pm.2 942s Introducing 14 SNPs, 0/4 ref/read gaps, and 1 rearrangements 942s Finished SNPs 942s Finished ref gaps 942s Finished read gaps 942s Mutating sequence Sim.pm.1 942s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 942s Finished SNPs 942s Finished ref gaps 942s Finished read gaps 942s Mutated reference genome to subject genome 942s SNPs introduced: 19 942s Reference gaps introduced: 0 942s Read gaps introduced: 4 942s Rearrangements introduced: 1 942s Created read sampler 942s Sampling 94 reads 942s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 942s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 942s parsing sequence Sim.pm.1... 942s parsing sequence Sim.pm.2... 942s Parsed 110 reference bases 943s *** Run 7 of 100 943s /usr/bin/bowtie2 --score-min L,6.50808020829541,3.28425632517868 --large-index --ma 9.94295296173124 --rfg 35.5850010331371 --trim5 9 --mp 8.38402859151477,7.57679125714454 -R 2 --cp-ival 1 --cp-min 4 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 943s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 943s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s Read 50 alignments... 943s Read 100 alignments... 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 943s 94 reads; of these: 943s 80 (85.11%) were paired; of these: 943s 80 (100.00%) aligned concordantly 0 times 943s 0 (0.00%) aligned concordantly exactly 1 time 943s 0 (0.00%) aligned concordantly >1 times 943s ---- 943s 80 pairs aligned concordantly 0 times; of these: 943s 1 (1.25%) aligned discordantly 1 time 943s ---- 943s 79 pairs aligned 0 times concordantly or discordantly; of these: 943s 158 mates make up the pairs; of these: 943s 136 (86.08%) aligned 0 times 943s 11 (6.96%) aligned exactly 1 time 943s 11 (6.96%) aligned >1 times 943s 14 (14.89%) were unpaired; of these: 943s 11 (78.57%) aligned 0 times 943s 3 (21.43%) aligned exactly 1 time 943s 0 (0.00%) aligned >1 times 943s 15.52% overall alignment rate 943s Read 150 alignments... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s AC 943s AC 943s Processing line... 943s Processing line... 943s GGGA 943s GGGA 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s AC 943s AC 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s AT 943s AT 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s GCAT 943s GCAT 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s GGGGAG 943s GGGGAG 943s Processing line... 943s CAAAGG 943s CAAAGG 943s Processing line... 943s Processing line... 943s Processing line... 943s GCGAACAAAGGGCCT 943s GCGAACAAAGGGCCT 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s CGAA 943s CGAA 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s GCGAACA 943s GCGAACA 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s GACAGGGGAGGCGAACAAAGGGCCTCGC 943s GACAGGGGAGGCGAACAAAGGGCCTCGC 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s GAGGCG 943s GAGGCG 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s GGCGAAC 943s GGCGAAC 943s Processing line... 943s Processing line... 943s AACAAA 943s AACAAA 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s GGGA 943s GGGA 943s Processing line... 943s Processing line... 943s Processing line... 943s AGATGGGACAGGGGAGGCGAACAAAGGGCCTCG 943s AGATGGGACAGGGGAGGCGAACAAAGGGCCTCG 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s AGATGGGACAGGGGAG 943s AGATGGGACAGGGGAG 943s Processing line... 943s Processing line... 943s CGAACAAAGGGCCTCG 943s CGAACAAAGGGCCTCG 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s CC 943s CC 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s AACAAAGGGCCTCG 943s AACAAAGGGCCTCG 943s Processing line... 943s Processing line... 943s GGGAGGCGAA 943s GGGAGGCGAA 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s AAC 943s AAC 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s CCT 943s CCT 943s Processing line... 943s Processing line... 943s CCG 943s CCG 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s GGCGAA 943s GGCGAA 943s Processing line... 943s Processing line... 943s CGA 943s CGA 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s Processing line... 943s AAA 943s AAA 943s Processing line... 943s --- Summary --- 943s Read 1 reference strings 943s Checked 27 alignments, 0 edits 943s --------------- 943s PASSED 943s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 943s /usr/bin/bowtie2 --score-min L,6.50808020829541,3.28425632517868 --large-index --ma 9.94295296173124 --rfg 35.5850010331371 --trim5 9 --mp 8.38402859151477,7.57679125714454 -R 2 --cp-ival 1 --cp-min 4 --qseq -p 3 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 943s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 943s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 943s 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 943s 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 943s 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 943s 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 943s 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 943s 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 943s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 943s 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 943s 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 943s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 943s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 943s 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 943s 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 943s 94 reads; of these: 943s 80 (85.11%) were paired; of these: 943s 80 (100.00%) aligned concordantly 0 times 943s 0 (0.00%) aligned concordantly exactly 1 time 943s 0 (0.00%) aligned concordantly >1 times 943s ---- 943s 80 pairs aligned concordantly 0 times; of these: 943s 1 (1.25%) aligned discordantly 1 time 943s ---- 943s 79 pairs aligned 0 times concordantly or discordantly; of these: 943s 158 mates make up the pairs; of these: 943s 136 (86.08%) aligned 0 times 943s 11 (6.96%) aligned exactly 1 time 943s 11 (6.96%) aligned >1 times 943s 14 (14.89%) were unpaired; of these: 943s 11 (78.57%) aligned 0 times 943s 3 (21.43%) aligned exactly 1 time 943s 0 (0.00%) aligned >1 times 943s 15.52% overall alignment rate 943s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 943s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 943s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 943s Flattened IUPAC characters 943s Mutating sequence Sim.pm.2 943s Introducing 6 SNPs, 2/0 ref/read gaps, and 2 rearrangements 943s Finished SNPs 943s Finished ref gaps 943s Finished read gaps 943s Mutating sequence Sim.pm.1 943s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 943s Finished SNPs 943s Finished ref gaps 943s Finished read gaps 943s Mutated reference genome to subject genome 943s SNPs introduced: 9 943s Reference gaps introduced: 2 943s Read gaps introduced: 1 943s Rearrangements introduced: 2 943s Created read sampler 943s Sampling 36 reads 943s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 943s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 943s parsing sequence Sim.pm.1... 943s parsing sequence Sim.pm.2... 943s Parsed 110 reference bases 943s *** Run 8 of 100 943s /usr/bin/bowtie2 --cp-min 5 --cp-ival 2 --mm --local --mp 6.61637672334538,6.29148830137053 --large-index --np 2 --norc --score-min L,6.63732038865436,3.67049212520562 --gbar 9 --n-ceil 0.0626908728520964,0.511357196124905 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 944s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 944s Warning: skipping read '7' because it was < 2 characters long 944s 36 reads; of these: 944s 36 (100.00%) were unpaired; of these: 944s 36 (100.00%) aligned 0 times 944s 0 (0.00%) aligned exactly 1 time 944s 0 (0.00%) aligned >1 times 944s 0.00% overall alignment rate 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s /usr/bin/bowtie2 --cp-min 5 --cp-ival 2 --mm --local --mp 6.61637672334538,6.29148830137053 --large-index --np 2 --norc --score-min L,6.63732038865436,3.67049212520562 --gbar 9 --n-ceil 0.0626908728520964,0.511357196124905 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s --- Summary --- 944s Read 1 reference strings 944s Checked 0 alignments, 0 edits 944s --------------- 944s PASSED 944s ALSO checking that bowtie2 and bowtie2-align match up 944s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 944s Warning: skipping read '7' because it was < 2 characters long 944s 36 reads; of these: 944s 36 (100.00%) were unpaired; of these: 944s 36 (100.00%) aligned 0 times 944s 0 (0.00%) aligned exactly 1 time 944s 0 (0.00%) aligned >1 times 944s 0.00% overall alignment rate 944s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 944s Flattened IUPAC characters 944s Mutating sequence Sim.pm.1 944s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 944s Finished SNPs 944s Finished ref gaps 944s Finished read gaps 944s Mutating sequence Sim.pm.2 944s Introducing 1 SNPs, 2/3 ref/read gaps, and 3 rearrangements 944s Finished SNPs 944s Finished ref gaps 944s Finished read gaps 944s Mutated reference genome to subject genome 944s SNPs introduced: 3 944s Reference gaps introduced: 2 944s Read gaps introduced: 4 944s Rearrangements introduced: 3 944s Created read sampler 944s Sampling 66 reads 944s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 944s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 944s parsing sequence Sim.pm.1... 944s parsing sequence Sim.pm.2... 944s Parsed 110 reference bases 944s *** Run 9 of 100 944s /usr/bin/bowtie2 --trim3 8 --local --large-index --cp-min 2 --mm --cp-ival 1 --rfg 35.1547880993025 --n-ceil 0.945607097994817,0.153317569071424 --gbar 2 --score-min L,3.32626393192095,4.94031127445701 -D 5 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 944s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 944s 66 reads; of these: 944s 66 (100.00%) were unpaired; of these: 944s 66 (100.00%) aligned 0 times 944s 0 (0.00%) aligned exactly 1 time 944s 0 (0.00%) aligned >1 times 944s 0.00% overall alignment rate 944s Read 50 alignments... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s Processing line... 944s --- Summary --- 944s Read 1 reference strings 944s Checked 0 alignments, 0 edits 944s --------------- 944s PASSED 944s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 944s /usr/bin/bowtie2 --trim3 8 --local --large-index --cp-min 2 --mm --cp-ival 1 --rfg 35.1547880993025 --n-ceil 0.945607097994817,0.153317569071424 --gbar 2 --score-min L,3.32626393192095,4.94031127445701 -D 5 --qseq -p 2 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 944s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 944s 66 reads; of these: 944s 66 (100.00%) were unpaired; of these: 944s 66 (100.00%) aligned 0 times 944s 0 (0.00%) aligned exactly 1 time 944s 0 (0.00%) aligned >1 times 944s 0.00% overall alignment rate 944s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 944s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 944s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 944s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 944s /usr/bin/bowtie2 --trim3 8 --local --large-index --cp-min 2 --mm --cp-ival 1 --rfg 35.1547880993025 --n-ceil 0.945607097994817,0.153317569071424 --gbar 2 --score-min L,3.32626393192095,4.94031127445701 -D 5 --qseq -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 944s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 944s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 944s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 944s 66 reads; of these: 944s 66 (100.00%) were unpaired; of these: 944s 66 (100.00%) aligned 0 times 944s 0 (0.00%) aligned exactly 1 time 944s 0 (0.00%) aligned >1 times 944s 0.00% overall alignment rate 944s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 944s Flattened IUPAC characters 944s Mutating sequence Sim.pm.1 944s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 944s Finished SNPs 944s Finished ref gaps 944s Finished read gaps 944s Mutating sequence Sim.pm.2 944s Introducing 13 SNPs, 0/0 ref/read gaps, and 1 rearrangements 944s Finished SNPs 944s Finished ref gaps 944s Finished read gaps 944s Mutated reference genome to subject genome 944s SNPs introduced: 17 944s Reference gaps introduced: 1 944s Read gaps introduced: 0 944s Rearrangements introduced: 2 944s Created read sampler 944s Sampling 40 reads 944s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 944s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 944s parsing sequence Sim.pm.1... 944s parsing sequence Sim.pm.2... 944s Parsed 110 reference bases 944s *** Run 10 of 100 944s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 8 --large-index --n-ceil 0.801570244894117,0.92316316485818 --score-min L,1.75320752152365,9.72637928125553 -a --mp 7.69949649481904,1.13079601671438 --rdg 14.3312097667497,8.63140785352777 --trim5 9 --local --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 945s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 945s 40 reads; of these: 945s 35 (87.50%) were paired; of these: 945s 35 (100.00%) aligned concordantly 0 times 945s 0 (0.00%) aligned concordantly exactly 1 time 945s 0 (0.00%) aligned concordantly >1 times 945s ---- 945s 35 pairs aligned concordantly 0 times; of these: 945s 0 (0.00%) aligned discordantly 1 time 945s ---- 945s 35 pairs aligned 0 times concordantly or discordantly; of these: 945s 70 mates make up the pairs; of these: 945s 70 (100.00%) aligned 0 times 945s 0 (0.00%) aligned exactly 1 time 945s 0 (0.00%) aligned >1 times 945s 5 (12.50%) were unpaired; of these: 945s 5 (100.00%) aligned 0 times 945s 0 (0.00%) aligned exactly 1 time 945s 0 (0.00%) aligned >1 times 945s 0.00% overall alignment rate 945s Read 50 alignments... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 8 --large-index --n-ceil 0.801570244894117,0.92316316485818 --score-min L,1.75320752152365,9.72637928125553 -a --mp 7.69949649481904,1.13079601671438 --rdg 14.3312097667497,8.63140785352777 --trim5 9 --local --qseq -p 3 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s --- Summary --- 945s Read 1 reference strings 945s Checked 0 alignments, 0 edits 945s --------------- 945s PASSED 945s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 945s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 945s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 945s 40 reads; of these: 945s 35 (87.50%) were paired; of these: 945s 35 (100.00%) aligned concordantly 0 times 945s 0 (0.00%) aligned concordantly exactly 1 time 945s 0 (0.00%) aligned concordantly >1 times 945s ---- 945s 35 pairs aligned concordantly 0 times; of these: 945s 0 (0.00%) aligned discordantly 1 time 945s ---- 945s 35 pairs aligned 0 times concordantly or discordantly; of these: 945s 70 mates make up the pairs; of these: 945s 70 (100.00%) aligned 0 times 945s 0 (0.00%) aligned exactly 1 time 945s 0 (0.00%) aligned >1 times 945s 5 (12.50%) were unpaired; of these: 945s 5 (100.00%) aligned 0 times 945s 0 (0.00%) aligned exactly 1 time 945s 0 (0.00%) aligned >1 times 945s 0.00% overall alignment rate 945s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 945s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 945s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 945s Flattened IUPAC characters 945s Mutating sequence Sim.pm.1 945s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 945s Finished SNPs 945s Finished ref gaps 945s Finished read gaps 945s Mutating sequence Sim.pm.2 945s Introducing 9 SNPs, 1/0 ref/read gaps, and 0 rearrangements 945s Finished SNPs 945s Finished ref gaps 945s Finished read gaps 945s Mutated reference genome to subject genome 945s SNPs introduced: 9 945s Reference gaps introduced: 1 945s Read gaps introduced: 0 945s Rearrangements introduced: 0 945s Created read sampler 945s Sampling 22 reads 945s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 945s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 945s *** Run 11 of 100 945s /usr/bin/bowtie2 --nofw --np 5 --score-min L,9.96662611847893,8.02733233353274 --gbar 3 -i L,0.302918269880141 --cp-ival 2 --cp-min 4 --large-index -M 2 --local --mp 8.47414557929261,3.54099195077285 --trim3 1 --rdg 15.4517301728004 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 945s parsing sequence Sim.pm.1... 945s parsing sequence Sim.pm.2... 945s Parsed 110 reference bases 945s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 945s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read '1' because it was < 2 characters long 945s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read '21' because it was < 2 characters long 945s 22 reads; of these: 945s 22 (100.00%) were paired; of these: 945s 22 (100.00%) aligned concordantly 0 times 945s 0 (0.00%) aligned concordantly exactly 1 time 945s 0 (0.00%) aligned concordantly >1 times 945s ---- 945s 22 pairs aligned concordantly 0 times; of these: 945s 0 (0.00%) aligned discordantly 1 time 945s ---- 945s 22 pairs aligned 0 times concordantly or discordantly; of these: 945s 44 mates make up the pairs; of these: 945s 44 (100.00%) aligned 0 times 945s 0 (0.00%) aligned exactly 1 time 945s 0 (0.00%) aligned >1 times 945s 0.00% overall alignment rate 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s Processing line... 945s --- Summary --- 945s Read 1 reference strings 945s Checked 0 alignments, 0 edits 945s --------------- 945s PASSED 945s ALSO checking that bowtie2 and bowtie2-align match up 945s /usr/bin/bowtie2 --nofw --np 5 --score-min L,9.96662611847893,8.02733233353274 --gbar 3 -i L,0.302918269880141 --cp-ival 2 --cp-min 4 --large-index -M 2 --local --mp 8.47414557929261,3.54099195077285 --trim3 1 --rdg 15.4517301728004 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 945s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 945s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read '1' because it was < 2 characters long 945s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 945s Warning: skipping mate #1 of read '21' because it was < 2 characters long 945s 22 reads; of these: 945s 22 (100.00%) were paired; of these: 945s 22 (100.00%) aligned concordantly 0 times 945s 0 (0.00%) aligned concordantly exactly 1 time 945s 0 (0.00%) aligned concordantly >1 times 945s ---- 945s 22 pairs aligned concordantly 0 times; of these: 945s 0 (0.00%) aligned discordantly 1 time 945s ---- 945s 22 pairs aligned 0 times concordantly or discordantly; of these: 945s 44 mates make up the pairs; of these: 945s 44 (100.00%) aligned 0 times 945s 0 (0.00%) aligned exactly 1 time 945s 0 (0.00%) aligned >1 times 945s 0.00% overall alignment rate 945s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 945s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 945s /usr/bin/bowtie2 --nofw --np 5 --score-min L,9.96662611847893,8.02733233353274 --gbar 3 -i L,0.302918269880141 --cp-ival 2 --cp-min 4 --large-index -M 2 --local --mp 8.47414557929261,3.54099195077285 --trim3 1 --rdg 15.4517301728004 -f -p 2 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 946s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 946s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 946s Warning: skipping mate #1 of read '1' because it was < 2 characters long 946s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 946s Warning: skipping mate #1 of read '21' because it was < 2 characters long 946s 22 reads; of these: 946s 22 (100.00%) were paired; of these: 946s 22 (100.00%) aligned concordantly 0 times 946s 0 (0.00%) aligned concordantly exactly 1 time 946s 0 (0.00%) aligned concordantly >1 times 946s ---- 946s 22 pairs aligned concordantly 0 times; of these: 946s 0 (0.00%) aligned discordantly 1 time 946s ---- 946s 22 pairs aligned 0 times concordantly or discordantly; of these: 946s 44 mates make up the pairs; of these: 946s 44 (100.00%) aligned 0 times 946s 0 (0.00%) aligned exactly 1 time 946s 0 (0.00%) aligned >1 times 946s 0.00% overall alignment rate 946s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 946s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 946s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 946s Flattened IUPAC characters 946s Mutating sequence Sim.pm.2 946s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 946s Finished SNPs 946s Finished ref gaps 946s Finished read gaps 946s Mutating sequence Sim.pm.1 946s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 946s Finished SNPs 946s Finished ref gaps 946s Finished read gaps 946s Mutated reference genome to subject genome 946s SNPs introduced: 3 946s Reference gaps introduced: 1 946s Read gaps introduced: 0 946s Rearrangements introduced: 0 946s Created read sampler 946s Sampling 30 reads 946s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 946s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 946s *** Run 12 of 100 946s /usr/bin/bowtie2 --n-ceil 0.60074248144548,1.23057794715237 --score-min L,2.53839983361028,5.72339192102119 --np 5 --nofw --norc --large-index --mp 6.9319998394791,4.32662518032041 --trim3 1 --cp-ival 8 --mm --cp-min 2 -f -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta 946s parsing sequence Sim.pm.1... 946s parsing sequence Sim.pm.2... 946s Parsed 110 reference bases 946s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 946s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 946s Warning: skipping read '7' because it was < 2 characters long 946s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 946s 30 reads; of these: 946s 30 (100.00%) were unpaired; of these: 946s 30 (100.00%) aligned 0 times 946s 0 (0.00%) aligned exactly 1 time 946s 0 (0.00%) aligned >1 times 946s 0.00% overall alignment rate 946s Processing line... 946s /usr/bin/bowtie2 --n-ceil 0.60074248144548,1.23057794715237 --score-min L,2.53839983361028,5.72339192102119 --np 5 --nofw --norc --large-index --mp 6.9319998394791,4.32662518032041 --trim3 1 --cp-ival 8 --mm --cp-min 2 -f -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s Processing line... 946s --- Summary --- 946s Read 1 reference strings 946s Checked 0 alignments, 0 edits 946s --------------- 946s PASSED 946s ALSO checking that bowtie2 and bowtie2-align match up 946s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 946s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 946s Warning: skipping read '7' because it was < 2 characters long 946s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 946s 30 reads; of these: 946s 30 (100.00%) were unpaired; of these: 946s 30 (100.00%) aligned 0 times 946s 0 (0.00%) aligned exactly 1 time 946s 0 (0.00%) aligned >1 times 946s 0.00% overall alignment rate 946s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 946s /usr/bin/bowtie2 --n-ceil 0.60074248144548,1.23057794715237 --score-min L,2.53839983361028,5.72339192102119 --np 5 --nofw --norc --large-index --mp 6.9319998394791,4.32662518032041 --trim3 1 --cp-ival 8 --mm --cp-min 2 -f -p 3 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 946s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 946s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 946s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 946s Warning: skipping read '7' because it was < 2 characters long 946s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 946s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 946s 30 reads; of these: 946s 30 (100.00%) were unpaired; of these: 946s 30 (100.00%) aligned 0 times 946s 0 (0.00%) aligned exactly 1 time 946s 0 (0.00%) aligned >1 times 946s 0.00% overall alignment rate 946s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 946s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 946s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 946s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 946s /usr/bin/bowtie2 --n-ceil 0.60074248144548,1.23057794715237 --score-min L,2.53839983361028,5.72339192102119 --np 5 --nofw --norc --large-index --mp 6.9319998394791,4.32662518032041 --trim3 1 --cp-ival 8 --mm --cp-min 2 -f -p 4 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 947s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 947s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 947s Warning: skipping read '7' because it was < 2 characters long 947s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 947s 30 reads; of these: 947s 30 (100.00%) were unpaired; of these: 947s 30 (100.00%) aligned 0 times 947s 0 (0.00%) aligned exactly 1 time 947s 0 (0.00%) aligned >1 times 947s 0.00% overall alignment rate 947s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 947s Flattened IUPAC characters 947s Mutating sequence Sim.pm.2 947s Introducing 14 SNPs, 1/2 ref/read gaps, and 1 rearrangements 947s Finished SNPs 947s Finished ref gaps 947s Finished read gaps 947s Mutating sequence Sim.pm.1 947s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 947s Finished SNPs 947s Finished ref gaps 947s Finished read gaps 947s Mutated reference genome to subject genome 947s SNPs introduced: 19 947s Reference gaps introduced: 1 947s Read gaps introduced: 2 947s Rearrangements introduced: 1 947s Created read sampler 947s *** Run 13 of 100 947s /usr/bin/bowtie2 --rfg 26.7872677468312 --score-min L,1.01929888438452,1.33043733010403 --np 18 --nofw --trim3 1 --ma 35.8388777064647 --large-index -k 6 --cp-min 15 --mm --cp-ival 1 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 947s Sampling 53 reads 947s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 947s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 947s parsing sequence Sim.pm.1... 947s parsing sequence Sim.pm.2... 947s Parsed 110 reference bases 947s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 947s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 947s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 947s 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 947s 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 947s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 947s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 947s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 947s 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 947s 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 947s 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 947s 53 reads; of these: 947s 53 (100.00%) were unpaired; of these: 947s 47 (88.68%) aligned 0 times 947s 5 (9.43%) aligned exactly 1 time 947s 1 (1.89%) aligned >1 times 947s 11.32% overall alignment rate 947s Read 50 alignments... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s CAG 947s CAG 947s Processing line... 947s CAG 947s CAG 947s Processing line... 947s CAG 947s CAG 947s Processing line... 947s CAG 947s CAG 947s Processing line... 947s CAG 947s CAG 947s /usr/bin/bowtie2 --rfg 26.7872677468312 --score-min L,1.01929888438452,1.33043733010403 --np 18 --nofw --trim3 1 --ma 35.8388777064647 --large-index -k 6 --cp-min 15 --mm --cp-ival 1 --qseq -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s GACGCACAGCATA 947s GACGCACAGCATA 947s Processing line... 947s Processing line... 947s Processing line... 947s GGACGCACAG 947s GGACGCACAG 947s Processing line... 947s TCGGG 947s TCGGG 947s Processing line... 947s Processing line... 947s Processing line... 947s TCGCA 947s TCGCA 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s ACAGCAT 947s ACAGCAT 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s --- Summary --- 947s Read 1 reference strings 947s Checked 10 alignments, 0 edits 947s --------------- 947s PASSED 947s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 947s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 947s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 947s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 947s 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 947s 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 947s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 947s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 947s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 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 947s 53 reads; of these: 947s 53 (100.00%) were unpaired; of these: 947s 47 (88.68%) aligned 0 times 947s 5 (9.43%) aligned exactly 1 time 947s 1 (1.89%) aligned >1 times 947s 11.32% overall alignment rate 947s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 947s Flattened IUPAC characters 947s Mutating sequence Sim.pm.2 947s Introducing 3 SNPs, 0/1 ref/read gaps, and 4 rearrangements 947s Finished SNPs 947s Finished ref gaps 947s Finished read gaps 947s Mutating sequence Sim.pm.1 947s Introducing 0 SNPs, 0/1 ref/read gaps, and 1 rearrangements 947s Finished SNPs 947s Finished ref gaps 947s Finished read gaps 947s Mutated reference genome to subject genome 947s SNPs introduced: 3 947s Reference gaps introduced: 0 947s Read gaps introduced: 2 947s Rearrangements introduced: 5 947s Created read sampler 947s Sampling 23 reads 947s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 947s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 947s parsing sequence Sim.pm.1... 947s parsing sequence Sim.pm.2... 947s Parsed 110 reference bases 947s *** Run 14 of 100 947s /usr/bin/bowtie2 --score-min L,9.57628010119489,3.10672033767739 --n-ceil 1.24952713922123,0.741690785411614 --large-index --ma 15.10037813407 --trim5 1 --trim3 2 --cp-ival 1 --nofw --cp-min 9 -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 947s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 947s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 947s Warning: skipping mate #1 of read '1' because it was < 2 characters long 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 947s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 947s Warning: skipping mate #1 of read '3' because it was < 2 characters long 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 947s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 947s Warning: skipping mate #1 of read '13' because it was < 2 characters long 947s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 947s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 947s 23 reads; of these: 947s 21 (91.30%) were paired; of these: 947s 21 (100.00%) aligned concordantly 0 times 947s 0 (0.00%) aligned concordantly exactly 1 time 947s 0 (0.00%) aligned concordantly >1 times 947s ---- 947s 21 pairs aligned concordantly 0 times; of these: 947s 0 (0.00%) aligned discordantly 1 time 947s ---- 947s 21 pairs aligned 0 times concordantly or discordantly; of these: 947s 42 mates make up the pairs; of these: 947s 36 (85.71%) aligned 0 times 947s 4 (9.52%) aligned exactly 1 time 947s 2 (4.76%) aligned >1 times 947s 2 (8.70%) were unpaired; of these: 947s 2 (100.00%) aligned 0 times 947s 0 (0.00%) aligned exactly 1 time 947s 0 (0.00%) aligned >1 times 947s 13.64% overall alignment rate 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s GGGCCTCGCAG 947s GGGCCTCGCAG 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s AG 947s AG 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s AAAGGGC 947s AAAGGGC 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s ACAGGGGAGG 947s ACAGGGGAGG 947s Processing line... 947s Processing line... 947s GGC 947s GGC 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s GTCCAGGGACGCACAGCATAGTGCGA 947s GTCCAGGGACGCACAGCATAGTGCGA 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s Processing line... 947s --- Summary --- 947s Read 1 reference strings 947s Checked 6 alignments, 0 edits 947s --------------- 947s PASSED 947s ALSO checking that bowtie2 and bowtie2-align match up 947s /usr/bin/bowtie2 --score-min L,9.57628010119489,3.10672033767739 --n-ceil 1.24952713922123,0.741690785411614 --large-index --ma 15.10037813407 --trim5 1 --trim3 2 --cp-ival 1 --nofw --cp-min 9 -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 947s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 948s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 948s Warning: skipping mate #1 of read '1' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 948s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 948s Warning: skipping mate #1 of read '3' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 948s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 948s Warning: skipping mate #1 of read '13' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 948s 23 reads; of these: 948s 21 (91.30%) were paired; of these: 948s 21 (100.00%) aligned concordantly 0 times 948s 0 (0.00%) aligned concordantly exactly 1 time 948s 0 (0.00%) aligned concordantly >1 times 948s ---- 948s 21 pairs aligned concordantly 0 times; of these: 948s 0 (0.00%) aligned discordantly 1 time 948s ---- 948s 21 pairs aligned 0 times concordantly or discordantly; of these: 948s 42 mates make up the pairs; of these: 948s 36 (85.71%) aligned 0 times 948s 4 (9.52%) aligned exactly 1 time 948s 2 (4.76%) aligned >1 times 948s 2 (8.70%) were unpaired; of these: 948s 2 (100.00%) aligned 0 times 948s 0 (0.00%) aligned exactly 1 time 948s 0 (0.00%) aligned >1 times 948s 13.64% overall alignment rate 948s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 948s Flattened IUPAC characters 948s Mutating sequence Sim.pm.1 948s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 948s Finished SNPs 948s Finished ref gaps 948s Finished read gaps 948s Mutating sequence Sim.pm.2 948s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 948s Finished SNPs 948s Finished ref gaps 948s Finished read gaps 948s Mutated reference genome to subject genome 948s SNPs introduced: 8 948s Reference gaps introduced: 1 948s Read gaps introduced: 0 948s Rearrangements introduced: 0 948s Created read sampler 948s Sampling 30 reads 948s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 948s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 948s parsing sequence Sim.pm.1... 948s *** Run 15 of 100 948s /usr/bin/bowtie2 --cp-min 3 --mm --cp-ival 3 --rdg 37.6204154392403 --mp 6.79656907855923,4.85343133590262 --local --large-index -k 5 --norc -R 4 --score-min L,7.91480350622828,6.70452701900378 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 948s parsing sequence Sim.pm.2... 948s Parsed 110 reference bases 948s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 948s Warning: skipping read '1' because it was < 2 characters long 948s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 948s Warning: skipping read '17' because it was < 2 characters long 948s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 948s Warning: skipping read '18' because it was < 2 characters long 948s 30 reads; of these: 948s 30 (100.00%) were unpaired; of these: 948s 30 (100.00%) aligned 0 times 948s 0 (0.00%) aligned exactly 1 time 948s 0 (0.00%) aligned >1 times 948s 0.00% overall alignment rate 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s Processing line... 948s --- Summary --- 948s Read 1 reference strings 948s Checked 0 alignments, 0 edits 948s --------------- 948s PASSED 948s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 948s /usr/bin/bowtie2 --cp-min 3 --mm --cp-ival 3 --rdg 37.6204154392403 --mp 6.79656907855923,4.85343133590262 --local --large-index -k 5 --norc -R 4 --score-min L,7.91480350622828,6.70452701900378 -r -p 4 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 948s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 948s Warning: skipping read '1' because it was < 2 characters long 948s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 948s Warning: skipping read '17' because it was < 2 characters long 948s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 948s Warning: skipping read '18' because it was < 2 characters long 948s 30 reads; of these: 948s 30 (100.00%) were unpaired; of these: 948s 30 (100.00%) aligned 0 times 948s 0 (0.00%) aligned exactly 1 time 948s 0 (0.00%) aligned >1 times 948s 0.00% overall alignment rate 948s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 948s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 948s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 948s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 948s /usr/bin/bowtie2 --cp-min 3 --mm --cp-ival 3 --rdg 37.6204154392403 --mp 6.79656907855923,4.85343133590262 --local --large-index -k 5 --norc -R 4 --score-min L,7.91480350622828,6.70452701900378 -r -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 948s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 948s Warning: skipping read '1' because it was < 2 characters long 948s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 948s Warning: skipping read '17' because it was < 2 characters long 948s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 948s Warning: skipping read '18' because it was < 2 characters long 948s 30 reads; of these: 948s 30 (100.00%) were unpaired; of these: 948s 30 (100.00%) aligned 0 times 948s 0 (0.00%) aligned exactly 1 time 948s 0 (0.00%) aligned >1 times 948s 0.00% overall alignment rate 948s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 948s Flattened IUPAC characters 948s Mutating sequence Sim.pm.2 948s Introducing 11 SNPs, 0/0 ref/read gaps, and 0 rearrangements 948s Finished SNPs 948s Finished ref gaps 948s Finished read gaps 948s Mutating sequence Sim.pm.1 948s Introducing 10 SNPs, 0/1 ref/read gaps, and 1 rearrangements 948s Finished SNPs 948s Finished ref gaps 948s Finished read gaps 948s Mutated reference genome to subject genome 948s SNPs introduced: 21 948s Reference gaps introduced: 0 948s Read gaps introduced: 1 948s Rearrangements introduced: 1 948s Created read sampler 948s Sampling 115 reads 948s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 948s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 948s parsing sequence Sim.pm.1... 948s parsing sequence Sim.pm.2... 948s Parsed 110 reference bases 948s *** Run 16 of 100 948s /usr/bin/bowtie2 --score-min L,6.32254503081382,2.25672408045342 --np 5 --rdg 27.5918001701604,16.841497089028 --trim3 6 -k 6 --ma 3.63412710693702 --large-index --cp-min 4 --cp-ival 2 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 948s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 948s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 948s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '3' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 948s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '5' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 948s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '8' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 948s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '9' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 948s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '15' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 948s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '16' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 948s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '20' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 948s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '25' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 948s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '27' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 948s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '30' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 948s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '35' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 948s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '37' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 948s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '43' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 948s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '46' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 948s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '47' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 948s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '58' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 948s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '59' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 948s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '65' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 948s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '68' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 948s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '69' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 948s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '70' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 948s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '74' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 948s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '89' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 948s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '93' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 948s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 948s Warning: skipping read '105' because it was < 2 characters long 948s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 948s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 948s 115 reads; of these: 948s 115 (100.00%) were unpaired; of these: 948s 98 (85.22%) aligned 0 times 948s 7 (6.09%) aligned exactly 1 time 948s 10 (8.70%) aligned >1 times 948s 14.78% overall alignment rate 948s Read 50 alignments... 948s Read 100 alignments... 948s Read 150 alignments... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s CA 949s CA 949s Processing line... 949s CA 949s CA 949s Processing line... 949s CA 949s CA 949s Processing line... 949s CA 949s CA 949s Processing line... 949s CA 949s CA 949s Processing line... 949s CA 949s CA 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s CGGAAGC 949s CGGAAGC 949s Processing line... 949s TCG 949s TCG 949s Processing line... 949s CGA 949s CGA 949s Processing line... 949s CGA 949s CGA 949s Processing line... 949s TCG 949s TCG 949s Processing line... 949s CGA 949s CGA 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s GCATAGTG 949s GCATAGTG 949s Processing line... 949s ATG 949s ATG 949s Processing line... 949s CAT 949s CAT 949s Processing line... 949s ATG 949s ATG 949s Processing line... 949s ATG 949s ATG 949s Processing line... 949s CAT 949s CAT 949s Processing line... 949s ATAGTGCGACCG 949s ATAGTGCGACCG 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s CG 949s CG 949s Processing line... 949s CG 949s CG 949s Processing line... 949s CG 949s CG 949s Processing line... 949s CG 949s CG 949s Processing line... 949s CG 949s CG 949s Processing line... 949s CG 949s CG 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s TCCAGGGACGCACAG 949s TCCAGGGACGCACAG 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s GACCGCGTC 949s GACCGCGTC 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s AG 949s AG 949s Processing line... 949s AG 949s AG 949s Processing line... 949s AG 949s AG 949s Processing line... 949s AG 949s AG 949s Processing line... 949s AG 949s AG 949s Processing line... 949s AG 949s AG 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s GGG 949s GGG 949s Processing line... 949s GGG 949s GGG 949s Processing line... 949s GGG 949s GGG 949s Processing line... 949s GGG 949s GGG 949s Processing line... 949s GGG 949s GGG 949s Processing line... 949s GGG 949s GGG 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s /usr/bin/bowtie2 --score-min L,6.32254503081382,2.25672408045342 --np 5 --rdg 27.5918001701604,16.841497089028 --trim3 6 -k 6 --ma 3.63412710693702 --large-index --cp-min 4 --cp-ival 2 -r -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s CGAATGCAGATGGGA 949s CGAATGCAGATGGGA 949s Processing line... 949s Processing line... 949s AGA 949s AGA 949s Processing line... 949s AGA 949s AGA 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s AGG 949s AGG 949s Processing line... 949s AGG 949s AGG 949s Processing line... 949s AGG 949s AGG 949s Processing line... 949s AGG 949s AGG 949s Processing line... 949s CCT 949s CCT 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s GGCGAA 949s GGCGAA 949s Processing line... 949s Processing line... 949s Processing line... 949s GCG 949s GCG 949s Processing line... 949s GCG 949s GCG 949s Processing line... 949s CGC 949s CGC 949s Processing line... 949s GCG 949s GCG 949s Processing line... 949s CGC 949s CGC 949s Processing line... 949s GCG 949s GCG 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s CGG 949s CGG 949s Processing line... 949s CGG 949s CGG 949s Processing line... 949s CCG 949s CCG 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s --- Summary --- 949s Read 1 reference strings 949s Checked 57 alignments, 0 edits 949s --------------- 949s PASSED 949s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 949s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 949s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 949s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '3' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 949s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '5' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 949s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '16' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 949s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '20' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 949s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '8' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 949s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '9' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 949s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '15' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 949s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '35' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 949s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '37' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 949s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '43' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 949s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '46' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 949s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '47' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 949s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '58' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 949s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '59' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 949s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '25' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 949s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '27' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 949s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '30' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 949s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '65' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 949s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '68' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 949s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '69' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 949s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '70' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 949s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '74' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 949s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '105' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 949s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '89' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 949s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 949s Warning: skipping read '93' because it was < 2 characters long 949s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 949s Warning: minimum score function gave posidiff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 949s *** Run 17 of 100 949s /usr/bin/bowtie2 --cp-ival 3 --mm --np 4 --cp-min 5 --score-min L,1.769438365196,7.05156139395326 --large-index -M 5 --rfg 6.50434752780457,2.26045012992726 --local --trim3 1 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 949s tive number in --end-to-end mode for read '78; setting to 0 instead 949s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 949s 115 reads; of these: 949s 115 (100.00%) were unpaired; of these: 949s 98 (85.22%) aligned 0 times 949s 7 (6.09%) aligned exactly 1 time 949s 10 (8.70%) aligned >1 times 949s 14.78% overall alignment rate 949s Flattened IUPAC characters 949s Mutating sequence Sim.pm.1 949s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 949s Finished SNPs 949s Finished ref gaps 949s Finished read gaps 949s Mutating sequence Sim.pm.2 949s Introducing 13 SNPs, 0/0 ref/read gaps, and 1 rearrangements 949s Finished SNPs 949s Finished ref gaps 949s Finished read gaps 949s Mutated reference genome to subject genome 949s SNPs introduced: 21 949s Reference gaps introduced: 1 949s Read gaps introduced: 0 949s Rearrangements introduced: 1 949s Created read sampler 949s Sampling 72 reads 949s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 949s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 949s parsing sequence Sim.pm.1... 949s parsing sequence Sim.pm.2... 949s Parsed 110 reference bases 949s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 949s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 949s Warning: skipping mate #1 of read '43' because it was < 2 characters long 949s Read 50 alignments... 949s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 949s Warning: skipping mate #2 of read '61' because it was < 2 characters long 949s 72 reads; of these: 949s 72 (100.00%) were paired; of these: 949s 72 (100.00%) aligned concordantly 0 times 949s 0 (0.00%) aligned concordantly exactly 1 time 949s 0 (0.00%) aligned concordantly >1 times 949s ---- 949s 72 pairs aligned concordantly 0 times; of these: 949s 0 (0.00%) aligned discordantly 1 time 949s ---- 949s 72 pairs aligned 0 times concordantly or discordantly; of these: 949s 144 mates make up the pairs; of these: 949s 144 (100.00%) aligned 0 times 949s 0 (0.00%) aligned exactly 1 time 949s 0 (0.00%) aligned >1 times 949s 0.00% overall alignment rate 949s Read 100 alignments... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s /usr/bin/bowtie2 --cp-ival 3 --mm --np 4 --cp-min 5 --score-min L,1.769438365196,7.05156139395326 --large-index -M 5 --rfg 6.50434752780457,2.26045012992726 --local --trim3 1 -f -p 3 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s Processing line... 949s --- Summary --- 949s Read 1 reference strings 949s Checked 0 alignments, 0 edits 949s --------------- 949s PASSED 949s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 949s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 949s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 949s Warning: skipping mate #1 of read '43' because it was < 2 characters long 949s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 949s Warning: skipping mate #2 of read '61' because it was < 2 characters long 949s 72 reads; of these: 949s 72 (100.00%) were paired; of these: 949s 72 (100.00%) aligned concordantly 0 times 949s 0 (0.00%) aligned concordantly exactly 1 time 949s 0 (0.00%) aligned concordantly >1 times 949s ---- 949s 72 pairs aligned concordantly 0 times; of these: 949s 0 (0.00%) aligned discordantly 1 time 949s ---- 949s 72 pairs aligned 0 times concordantly or discordantly; of these: 949s 144 mates make up the pairs; of these: 949s 144 (100.00%) aligned 0 times 949s 0 (0.00%) aligned exactly 1 time 949s 0 (0.00%) aligned >1 times 949s 0.00% overall alignment rate 949s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 949s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 949s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 949s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 949s /usr/bin/bowtie2 --cp-ival 3 --mm --np 4 --cp-min 5 --score-min L,1.769438365196,7.05156139395326 --large-index -M 5 --rfg 6.50434752780457,2.26045012992726 --local --trim3 1 -f -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 950s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 950s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 950s Warning: skipping mate #1 of read '43' because it was < 2 characters long 950s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 950s Warning: skipping mate #2 of read '61' because it was < 2 characters long 950s 72 reads; of these: 950s 72 (100.00%) were paired; of these: 950s 72 (100.00%) aligned concordantly 0 times 950s 0 (0.00%) aligned concordantly exactly 1 time 950s 0 (0.00%) aligned concordantly >1 times 950s ---- 950s 72 pairs aligned concordantly 0 times; of these: 950s 0 (0.00%) aligned discordantly 1 time 950s ---- 950s 72 pairs aligned 0 times concordantly or discordantly; of these: 950s 144 mates make up the pairs; of these: 950s 144 (100.00%) aligned 0 times 950s 0 (0.00%) aligned exactly 1 time 950s 0 (0.00%) aligned >1 times 950s 0.00% overall alignment rate 950s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 950s Flattened IUPAC characters 950s Mutating sequence Sim.pm.2 950s Introducing 9 SNPs, 1/2 ref/read gaps, and 0 rearrangements 950s Finished SNPs 950s Finished ref gaps 950s Finished read gaps 950s Mutating sequence Sim.pm.1 950s Introducing 5 SNPs, 0/1 ref/read gaps, and 1 rearrangements 950s Finished SNPs 950s Finished ref gaps 950s Finished read gaps 950s Mutated reference genome to subject genome 950s SNPs introduced: 14 950s Reference gaps introduced: 1 950s Read gaps introduced: 3 950s Rearrangements introduced: 1 950s Created read sampler 950s Sampling 43 reads 950s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 950s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 950s parsing sequence Sim.pm.1... 950s parsing sequence Sim.pm.2... 950s Parsed 110 reference bases 950s *** Run 18 of 100 950s /usr/bin/bowtie2 --score-min L,1.45022611798217,7.02624452916476 --large-index --rfg 2.71977792548999,7.56045004475781 -a --mp 7.57552977228539,4.58323951138899 --trim5 7 --cp-ival 1 --np 7 --cp-min 3 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 950s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 950s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '0' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 950s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '1' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 950s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '3' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 950s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '9' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 950s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '17' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 950s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '22' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 950s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '23' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 950s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '28' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 950s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '31' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 950s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '32' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 950s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '34' because it was < 2 characters long 950s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 950s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 950s 43 reads; of these: 950s 43 (100.00%) were unpaired; of these: 950s 33 (76.74%) aligned 0 times 950s 5 (11.63%) aligned exactly 1 time 950s 5 (11.63%) aligned >1 times 950s 23.26% overall alignment rate 950s Read 50 alignments... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s TGG 950s TGG 950s Processing line... 950s CCA 950s CCA 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s GGAG 950s GGAG 950s Processing line... 950s GAGGCG 950s GAGGCG 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s CAT 950s CAT 950s Processing line... 950s CAT 950s CAT 950s Processing line... 950s ATG 950s ATG 950s Processing line... 950s ATG 950s ATG 950s Processing line... 950s ATG 950s ATG 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s ATGGGAC 950s ATGGGAC 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s GGGACAGGGG 950s GGGACAGGGG 950s Processing line... 950s Processing line... 950s Processing line... 950s GTCCAGGGACGCACAGCATAGTGCGACCGCGT 950s GTCCAGGGACGCACAGCATAGTGCGACCGCGT 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s CA 950s CA 950s Processing line... 950s CA 950s CA 950s Processing line... 950s CA 950s CA 950s Processing line... 950s CA 950s CA 950s Processing line... 950s TG 950s TG 950s Processing line... 950s *** Run 19 of 100 950s /usr/bin/bowtie2 --mp 7.84150451865414,2.82471778248484 --rfg 41.6389480392964,12.6320332282795 --local --large-index -M 4 --score-min L,5.15914023179883,7.69100371549619 --cp-min 12 --np 1 --cp-ival 1 -r -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw 950s TG 950s TG 950s Processing line... 950s CA 950s CA 950s Processing line... 950s CA 950s CA 950s Processing line... 950s CA 950s CA 950s Processing line... 950s TG 950s TG 950s Processing line... 950s TG 950s TG 950s Processing line... 950s CA 950s CA 950s Processing line... 950s CA 950s CA 950s Processing line... 950s GA 950s GA 950s Processing line... 950s GA 950s GA 950s Processing line... 950s TC 950s TC 950s Processing line... 950s GA 950s GA 950s Processing line... 950s GA 950s GA 950s Processing line... 950s TC 950s TC 950s Processing line... 950s GA 950s GA 950s Processing line... 950s GA 950s GA 950s Processing line... 950s TC 950s TC 950s Processing line... 950s GA 950s GA 950s Processing line... 950s TC 950s TC 950s Processing line... 950s GA 950s GA 950s Processing line... 950s GA 950s GA 950s Processing line... 950s GA 950s GA 950s Processing line... 950s TA 950s TA 950s Processing line... 950s TA 950s TA 950s --- Summary --- 950s Read 1 reference strings 950s Checked 41 alignments, 0 edits 950s --------------- 950s PASSED 950s Flattened IUPAC characters 950s Mutating sequence Sim.pm.2 950s Introducing 0 SNPs, 2/1 ref/read gaps, and 2 rearrangements 950s Finished SNPs 950s Finished ref gaps 950s Finished read gaps 950s Mutating sequence Sim.pm.1 950s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 950s Finished SNPs 950s Finished ref gaps 950s Finished read gaps 950s Mutated reference genome to subject genome 950s SNPs introduced: 8 950s Reference gaps introduced: 2 950s Read gaps introduced: 1 950s Rearrangements introduced: 2 950s Created read sampler 950s Sampling 106 reads 950s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 950s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 950s parsing sequence Sim.pm.1... 950s parsing sequence Sim.pm.2... 950s Parsed 110 reference bases 950s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 950s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 950s Warning: skipping mate #2 of read '9' because it was < 2 characters long 950s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 950s Warning: skipping mate #1 of read '19' because it was < 2 characters long 950s Read 50 alignments... 950s Read 100 alignments... 950s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 950s Warning: skipping mate #1 of read '75' because it was < 2 characters long 950s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (0) 950s Warning: skipping mate #1 of read '82' because it was < 2 characters long 950s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 950s Warning: skipping mate #2 of read '85' because it was < 2 characters long 950s 106 reads; of these: 950s 106 (100.00%) were paired; of these: 950s 106 (100.00%) aligned concordantly 0 times 950s 0 (0.00%) aligned concordantly exactly 1 time 950s 0 (0.00%) aligned concordantly >1 times 950s ---- 950s 106 pairs aligned concordantly 0 times; of these: 950s 0 (0.00%) aligned discordantly 1 time 950s ---- 950s 106 pairs aligned 0 times concordantly or discordantly; of these: 950s 212 mates make up the pairs; of these: 950s 212 (100.00%) aligned 0 times 950s 0 (0.00%) aligned exactly 1 time 950s 0 (0.00%) aligned >1 times 950s 0.00% overall alignment rate 950s Read 150 alignments... 950s Read 200 alignments... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s --- Summary --- 950s Read 1 reference strings 950s Checked 0 alignments, 0 edits 950s --------------- 950s PASSED 950s Flattened IUPAC characters 950s Mutating sequence Sim.pm.1 950s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 950s Finished SNPs 950s Finished ref gaps 950s Finished read gaps 950s Mutating sequence Sim.pm.2 950s Introducing 16 SNPs, 0/1 ref/read gaps, and 1 rearrangements 950s Finished SNPs 950s Finished ref gaps 950s Finished read gaps 950s Mutated reference genome to subject genome 950s SNPs introduced: 19 950s Reference gaps introduced: 0 950s Read gaps introduced: 1 950s Rearrangements introduced: 2 950s Created read sampler 950s Sampling 89 reads 950s *** Run 20 of 100 950s /usr/bin/bowtie2 --rfg 23.0249227751598 -i L,0.422661079059444 --n-ceil 0.736233947602979,0.846345873987023 --score-min L,9.24802520083363,7.8779074901818 -R 2 -D 12 --trim3 4 --local --large-index --cp-min 2 --cp-ival 1 --mm -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 950s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 950s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 950s parsing sequence Sim.pm.1... 950s parsing sequence Sim.pm.2... 950s Parsed 110 reference bases 950s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '20' because it was < 2 characters long 950s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '22' because it was < 2 characters long 950s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 950s Warning: skipping read '24' because it was < 2 characters long 950s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '25' because it was < 2 characters long 950s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '26' because it was < 2 characters long 950s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '28' because it was < 2 characters long 950s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '39' because it was < 2 characters long 950s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '43' because it was < 2 characters long 950s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '50' because it was < 2 characters long 950s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '72' because it was < 2 characters long 950s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 950s Warning: skipping read '74' because it was < 2 characters long 950s 89 reads; of these: 950s 89 (100.00%) were unpaired; of these: 950s 89 (100.00%) aligned 0 times 950s 0 (0.00%) aligned exactly 1 time 950s 0 (0.00%) aligned >1 times 950s 0.00% overall alignment rate 950s Read 50 alignments... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s /usr/bin/bowtie2 --rfg 23.0249227751598 -i L,0.422661079059444 --n-ceil 0.736233947602979,0.846345873987023 --score-min L,9.24802520083363,7.8779074901818 -R 2 -D 12 --trim3 4 --local --large-index --cp-min 2 --cp-ival 1 --mm -r -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s Processing line... 950s --- Summary --- 950s Read 1 reference strings 950s Checked 0 alignments, 0 edits 950s --------------- 950s PASSED 950s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 951s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 951s Warning: skipping read '20' because it was < 2 characters long 951s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 951s Warning: skipping read '22' because it was < 2 characters long 951s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 951s Warning: skipping read '24' because it was < 2 characters long 951s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 951s Warning: skipping read '25' because it was < 2 characters long 951s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 951s Warning: skipping read '26' because it was < 2 characters long 951s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 951s Warning: skipping read '28' because it was < 2 characters long 951s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 951s Warning: skipping read '39' because it was < 2 characters long 951s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 951s Warning: skipping read '43' because it was < 2 characters long 951s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 951s Warning: skipping read '50' because it was < 2 characters long 951s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 951s Warning: skipping read '72' because it was < 2 characters long 951s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 951s Warning: skipping read '74' because it was < 2 characters long 951s 89 reads; of these: 951s 89 (100.00%) were unpaired; of these: 951s 89 (100.00%) aligned 0 times 951s 0 (0.00%) aligned exactly 1 time 951s 0 (0.00%) aligned >1 times 951s 0.00% overall alignment rate 951s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 951s Flattened IUPAC characters 951s Mutating sequence Sim.pm.1 951s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 951s Finished SNPs 951s Finished ref gaps 951s Finished read gaps 951s Mutating sequence Sim.pm.2 951s Introducing 16 SNPs, 1/1 ref/read gaps, and 1 rearrangements 951s Finished SNPs 951s Finished ref gaps 951s Finished read gaps 951s Mutated reference genome to subject genome 951s SNPs introduced: 24 951s Reference gaps introduced: 1 951s Read gaps introduced: 1 951s Rearrangements introduced: 1 951s Created read sampler 951s Sampling 100 reads 951s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 951s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 951s parsing sequence Sim.pm.1... 951s parsing sequence Sim.pm.2... 951s Parsed 110 reference bases 951s *** Run 21 of 100 951s /usr/bin/bowtie2 --n-ceil 0.628570331227257,0.264335440922767 --score-min L,7.91527367653244,6.33853830200422 --gbar 1 -i L,0.16547396572553 -R 1 --np 2 --nofw --large-index --mp 5.66686516007573,3.63434240451041 --rdg 33.868554311724,11.4312409449627 --cp-ival 1 --cp-min 2 -r -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 951s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '2' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 951s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '8' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 951s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '20' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 951s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '38' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 951s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '42' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 951s Read 50 alignments... 951s Read 100 alignments... 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 951s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '66' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 951s Warning: skipping mate #2 of read '84' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #2 of read '84' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 951s 100 reads; of these: 951s 100 (100.00%) were paired; of these: 951s 99 (99.00%) aligned concordantly 0 times 951s 0 (0.00%) aligned concordantly exactly 1 time 951s 1 (1.00%) aligned concordantly >1 times 951s ---- 951s 99 pairs aligned concordantly 0 times; of these: 951s 0 (0.00%) aligned discordantly 1 time 951s ---- 951s 99 pairs aligned 0 times concordantly or discordantly; of these: 951s 198 mates make up the pairs; of these: 951s 180 (90.91%) aligned 0 times 951s 13 (6.57%) aligned exactly 1 time 951s 5 (2.53%) aligned >1 times 951s 10.00% overall alignment rate 951s Read 150 alignments... 951s Read 200 alignments... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s AAA 951s AAA 951s Processing line... 951s CGG 951s CGG 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s GGC 951s GGC 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s AACAAAGGGCCTCGCAGCGGAAG 951s AACAAAGGGCCTCGCAGCGGAAG 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s GT 951s GT 951s Processing line... 951s Processing line... 951s CGC 951s CGC 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s GCCTC 951s GCCTC 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s CGCACAG 951s CGCACAG 951s Processing line... 951s Processing line... 951s AGT 951s AGT 951s Processing line... 951s Processing line... 951s /usr/bin/bowtie2 --n-ceil 0.628570331227257,0.264335440922767 --score-min L,7.91527367653244,6.33853830200422 --gbar 1 -i L,0.16547396572553 -R 1 --np 2 --nofw --large-index --mp 5.66686516007573,3.63434240451041 --rdg 33.868554311724,11.4312409449627 --cp-ival 1 --cp-min 2 -r -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s CATAGT 951s CATAGT 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s TAG 951s TAG 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s AGGGG 951s AGGGG 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s CACAGCATAGTGCG 951s CACAGCATAGTGCG 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s GT 951s GT 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s GGA 951s GGA 951s Processing line... 951s AATGCAGATG 951s AATGCAGATG 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s GCGAACAAAGGGCCTCGC 951s GCGAACAAAGGGCCTCGC 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s GCAGCG 951s GCAGCG 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s AGGGGAGGCGAA 951s AGGGGAGGCGAA 951s Processing line... 951s Processing line... 951s AGTGCGACCGC 951s AGTGCGACCGC 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s Processing line... 951s --- Summary --- 951s Read 1 reference strings 951s Checked 20 alignments, 0 edits 951s --------------- 951s PASSED 951s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 951s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '2' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 951s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '8' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 951s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '20' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 951s Warning: skipping mate #2 of read '84' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #2 of read '84' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 951s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '38' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 951s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '42' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 951s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 951s Warning: skipping mate #1 of read '66' because it was < 2 characters long 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 951s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 951s 100 reads; of these: 951s 100 (100.00%) were paired; of these: 951s 99 (99.00%) aligned concordantly 0 times 951s 0 (0.00%) aligned concordantly exactly 1 time 951s 1 (1.00%) aligned concordantly >1 times 951s ---- 951s 99 pairs aligned concordantly 0 times; of these: 951s 0 (0.00%) aligned discordantly 1 time 951s ---- 951s 99 pairs aligned 0 times concordantly or discordantly; of these: 951s 198 mates make up the pairs; of these: 951s 180 (90.91%) aligned 0 times 951s 13 (6.57%) aligned exactly 1 time 951s 5 (2.53%) aligned >1 times 951s 10.00% overall alignment rate 951s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 951s Flattened IUPAC characters 951s Mutating sequence Sim.pm.1 951s Introducing 7 SNPs, 0/3 ref/read gaps, and 1 rearrangements 951s Finished SNPs 951s Finished ref gaps 951s Finished read gaps 951s Mutating sequence Sim.pm.2 951s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 951s Finished SNPs 951s Finished ref gaps 951s Finished read gaps 951s Mutated reference genome to subject genome 951s SNPs introduced: 12 951s Reference gaps introduced: 1 951s Read gaps introduced: 3 951s Rearrangements introduced: 1 951s Created read sampler 951s Sampling 95 reads 951s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 951s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 951s parsing sequence Sim.pm.1... 951s parsing sequence Sim.pm.2... 951s Parsed 110 reference bases 951s *** Run 22 of 100 951s /usr/bin/bowtie2 --cp-ival 1 --mm --np 1 --cp-min 3 --score-min L,8.13206192535593,9.3135540339407 --large-index --local --mp 8.39330982297256,1.93498064087394 -a --rdg 14.7148640843869 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 952s 95 reads; of these: 952s 95 (100.00%) were unpaired; of these: 952s 95 (100.00%) aligned 0 times 952s 0 (0.00%) aligned exactly 1 time 952s 0 (0.00%) aligned >1 times 952s 0.00% overall alignment rate 952s Read 50 alignments... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s --- Summary --- 952s Read 1 reference strings 952s Checked 0 alignments, 0 edits 952s --------------- 952s PASSED 952s ALSO checking that bowtie2 and bowtie2-align match up 952s /usr/bin/bowtie2 --cp-ival 1 --mm --np 1 --cp-min 3 --score-min L,8.13206192535593,9.3135540339407 --large-index --local --mp 8.39330982297256,1.93498064087394 -a --rdg 14.7148640843869 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 952s 95 reads; of these: 952s 95 (100.00%) were unpaired; of these: 952s 95 (100.00%) aligned 0 times 952s 0 (0.00%) aligned exactly 1 time 952s 0 (0.00%) aligned >1 times 952s 0.00% overall alignment rate 952s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 952s Flattened IUPAC characters 952s Mutating sequence Sim.pm.1 952s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 952s Finished SNPs 952s Finished ref gaps 952s Finished read gaps 952s Mutating sequence Sim.pm.2 952s Introducing 9 SNPs, 0/1 ref/read gaps, and 2 rearrangements 952s Finished SNPs 952s Finished ref gaps 952s Finished read gaps 952s Mutated reference genome to subject genome 952s SNPs introduced: 10 952s Reference gaps introduced: 1 952s Read gaps introduced: 1 952s Rearrangements introduced: 3 952s Created read sampler 952s Sampling 87 reads 952s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 952s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 952s parsing sequence Sim.pm.1... 952s parsing sequence Sim.pm.2... 952s Parsed 110 reference bases 952s *** Run 23 of 100 952s /usr/bin/bowtie2 --score-min L,8.85478497094322,1.83426826489754 --rfg 30.6443192059021 --norc --large-index -M 7 --mp 6.11489517323956,2.9876189455146 --local --mm --cp-ival 1 --cp-min 2 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 952s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 952s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 952s Warning: skipping read '56' because it was < 2 characters long 952s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 952s Warning: skipping read '65' because it was < 2 characters long 952s Warning: skipping read '75' because length (1) <= # seed mismatches (0) 952s Warning: skipping read '75' because it was < 2 characters long 952s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 952s Warning: skipping read '79' because it was < 2 characters long 952s 87 reads; of these: 952s 87 (100.00%) were unpaired; of these: 952s 87 (100.00%) aligned 0 times 952s 0 (0.00%) aligned exactly 1 time 952s 0 (0.00%) aligned >1 times 952s 0.00% overall alignment rate 952s Read 50 alignments... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s Processing line... 952s --- Summary --- 952s Read 1 reference strings 952s Checked 0 alignments, 0 edits 952s --------------- 952s PASSED 952s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 952s /usr/bin/bowtie2 --score-min L,8.85478497094322,1.83426826489754 --rfg 30.6443192059021 --norc --large-index -M 7 --mp 6.11489517323956,2.9876189455146 --local --mm --cp-ival 1 --cp-min 2 -r -p 4 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 952s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 952s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 952s Warning: skipping read '56' because it was < 2 characters long 952s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 952s Warning: skipping read '65' because it was < 2 characters long 952s Warning: skipping read '75' because length (1) <= # seed mismatches (0) 952s Warning: skipping read '75' because it was < 2 characters long 952s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 952s Warning: skipping read '79' because it was < 2 characters long 952s 87 reads; of these: 952s 87 (100.00%) were unpaired; of these: 952s 87 (100.00%) aligned 0 times 952s 0 (0.00%) aligned exactly 1 time 952s 0 (0.00%) aligned >1 times 952s 0.00% overall alignment rate 952s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 952s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 952s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 952s Flattened IUPAC characters 952s Mutating sequence Sim.pm.1 952s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 952s Finished SNPs 952s Finished ref gaps 952s Finished read gaps 952s Mutating sequence Sim.pm.2 952s Introducing 10 SNPs, 1/0 ref/read gaps, and 1 rearrangements 952s Finished SNPs 952s Finished ref gaps 952s Finished read gaps 952s Mutated reference genome to subject genome 952s SNPs introduced: 10 952s Reference gaps introduced: 1 952s Read gaps introduced: 0 952s Rearrangements introduced: 1 952s Created read sampler 952s Sampling 74 reads 952s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 952s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 952s parsing sequence Sim.pm.1... 952s parsing sequence Sim.pm.2... 952s Parsed 110 reference bases 952s *** Run 24 of 100 952s /usr/bin/bowtie2 --trim5 4 --score-min L,7.82719298000979,8.80690941148778 --norc --np 1 -D 49 -N 0 -L31 --local --large-index --cp-min 6 --cp-ival 1 -f -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta 953s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '1' because it was < 2 characters long 953s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '6' because it was < 2 characters long 953s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '7' because it was < 2 characters long 953s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '13' because it was < 2 characters long 953s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '18' because it was < 2 characters long 953s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '22' because it was < 2 characters long 953s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '29' because it was < 2 characters long 953s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '33' because it was < 2 characters long 953s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '38' because it was < 2 characters long 953s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '39' because it was < 2 characters long 953s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '42' because it was < 2 characters long 953s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '57' because it was < 2 characters long 953s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '69' because it was < 2 characters long 953s 74 reads; of these: 953s 74 (100.00%) were unpaired; of these: 953s 74 (100.00%) aligned 0 times 953s 0 (0.00%) aligned exactly 1 time 953s 0 (0.00%) aligned >1 times 953s 0.00% overall alignment rate 953s Read 50 alignments... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s --- Summary --- 953s Read 1 reference strings 953s Checked 0 alignments, 0 edits 953s --------------- 953s PASSED 953s Flattened IUPAC characters 953s Mutating sequence Sim.pm.2 953s Introducing 16 SNPs, 0/0 ref/read gaps, and 0 rearrangements 953s Finished SNPs 953s Finished ref gaps 953s Finished read gaps 953s Mutating sequence Sim.pm.1 953s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 953s Finished SNPs 953s Finished ref gaps 953s Finished read gaps 953s Mutated reference genome to subject genome 953s SNPs introduced: 16 953s Reference gaps introduced: 0 953s Read gaps introduced: 1 953s Rearrangements introduced: 0 953s Created read sampler 953s Sampling 92 reads 953s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 953s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 953s parsing sequence Sim.pm.1... 953s parsing sequence Sim.pm.2... 953s Parsed 110 reference bases 953s *** Run 25 of 100 953s /usr/bin/bowtie2 --rfg 12.4535137063585 --score-min L,2.67670891085652,1.25386713704965 --np 3 --mp 7.9722453279611,7.84664961600919 --trim3 2 --local --large-index -M 6 --cp-min 2 --mm --cp-ival 1 -f -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta 953s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 953s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '6' because it was < 2 characters long 953s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '12' because it was < 2 characters long 953s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '17' because it was < 2 characters long 953s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '38' because it was < 2 characters long 953s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '60' because it was < 2 characters long 953s Warning: skipping read '75' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '75' because it was < 2 characters long 953s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '88' because it was < 2 characters long 953s 92 reads; of these: 953s 92 (100.00%) were unpaired; of these: 953s 76 (82.61%) aligned 0 times 953s 15 (16.30%) aligned exactly 1 time 953s 1 (1.09%) aligned >1 times 953s 17.39% overall alignment rate 953s Read 50 alignments... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s GGGGGCGCATGTCCAGGGACGCACAG 953s GGGGNCGCATGTCCAGGGACGCACAG 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s CACAGCATAGTGCGACCGCGTCGGCTCGGG-A 953s CACAGCATAGTGCGACCGCGTCNGCTCGGGAA 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s CTCGCAG 953s CTCGCAG 953s Processing line... 953s CAGGGGAG 953s CAGGGGAG 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s CAAAGGGCCTCGCAGCG 953s CAAAGGGCCTCGCAGCG 953s Processing line... 953s Processing line... 953s Processing line... 953s GCACAGCATAGTGCG 953s GCACAGCATAGTGCG 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s GGGAGGCGAACAATGGGCCTCGCAGC 953s GGGAGGCGAACAAAGGGCCTCGCAGC 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s GGGACGCACAGCA 953s GGGACGCACAGCA 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s GAATGCAGAAGGGACAGGG 953s GAATGCAGATGGGACAGGG 953s Processing line... 953s Processing line... 953s GCCTC 953s GCCTC 953s Processing line... 953s Processing line... 953s GGGAGGCGATCAAAGGGCCTCGCAGCGGAAGC 953s GGGAGGCGAACAAAGGGCCTCGCAGCGGAAGC 953s /usr/bin/bowtie2 --rfg 12.4535137063585 --score-min L,2.67670891085652,1.25386713704965 --np 3 --mp 7.9722453279611,7.84664961600919 --trim3 2 --local --large-index -M 6 --cp-min 2 --mm --cp-ival 1 -f -p 3 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s TCGCAGCGGAA 953s TCGCAGCGGAA 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s ACAGCATAGTGCGACC 953s ACAGCATAGTGCGACC 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s GAGGCGATCAAAGGGC 953s GAGGCGAACAAAGGGC 953s Processing line... 953s CAGGGACGCACAGCATAG 953s CAGGGACGCACAGCATAG 953s Processing line... 953s Processing line... 953s Processing line... 953s Processing line... 953s GGACGCACAG 953s GGACGCACAG 953s Processing line... 953s --- Summary --- 953s Read 1 reference strings 953s Checked 16 alignments, 0 edits 953s --------------- 953s PASSED 953s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 953s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 953s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '17' because it was < 2 characters long 953s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '6' because it was < 2 characters long 953s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '12' because it was < 2 characters long 953s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '60' because it was < 2 characters long 953s Warning: skipping read '75' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '75' because it was < 2 characters long 953s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '88' because it was < 2 characters long 953s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '38' because it was < 2 characters long 953s 92 reads; of these: 953s 92 (100.00%) were unpaired; of these: 953s 76 (82.61%) aligned 0 times 953s 15 (16.30%) aligned exactly 1 time 953s 1 (1.09%) aligned >1 times 953s 17.39% overall alignment rate 953s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 953s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 953s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 953s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 953s /usr/bin/bowtie2 --rfg 12.4535137063585 --score-min L,2.67670891085652,1.25386713704965 --np 3 --mp 7.9722453279611,7.84664961600919 --trim3 2 --local --large-index -M 6 --cp-min 2 --mm --cp-ival 1 -f -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 953s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 953s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '17' because it was < 2 characters long 953s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '6' because it was < 2 characters long 953s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '12' because it was < 2 characters long 953s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '60' because it was < 2 characters long 953s Warning: skipping read '75' because length (1) <= # seed mismatches (0) 953s Warning: skipping read '75' because it was < 2 characters long 953s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '88' because it was < 2 characters long 953s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 953s Warning: skipping read '38' because it was < 2 characters long 953s 92 reads; of these: 953s 92 (100.00%) were unpaired; of these: 953s 76 (82.61%) aligned 0 times 953s 15 (16.30%) aligned exactly 1 time 953s 1 (1.09%) aligned >1 times 953s 17.39% overall alignment rate 953s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 953s Flattened IUPAC characters 953s Mutating sequence Sim.pm.2 953s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 953s Finished SNPs 953s Finished ref gaps 953s Finished read gaps 953s Mutating sequence Sim.pm.1 953s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 953s Finished SNPs 953s Finished ref gaps 953s Finished read gaps 953s Mutated reference genome to subject genome 953s SNPs introduced: 4 953s Reference gaps introduced: 0 953s Read gaps introduced: 0 953s Rearrangements introduced: 0 953s Created read sampler 953s Sampling 105 reads 953s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 953s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 953s parsing sequence Sim.pm.1... 953s *** Run 26 of 100 953s /usr/bin/bowtie2 --large-index --score-min L,6.03035959442172,8.46511495836767 --rdg 28.0117598525247,2.32672796341212 --rfg 19.1893959544127 -D 21 --cp-ival 1 --cp-min 5 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 953s parsing sequence Sim.pm.2... 953s Parsed 110 reference bases 954s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 954s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 954s Warning: skipping read '10' because it was < 2 characters long 954s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 954s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 954s Warning: skipping read '57' because it was < 2 characters long 954s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 954s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 954s Warning: skipping read '92' because it was < 2 characters long 954s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 954s 105 reads; of these: 954s 105 (100.00%) were unpaired; of these: 954s 84 (80.00%) aligned 0 times 954s 14 (13.33%) aligned exactly 1 time 954s 7 (6.67%) aligned >1 times 954s 20.00% overall alignment rate 954s Read 50 alignments... 954s Read 100 alignments... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s GGCGAACAAA 954s GGCGAACAAA 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s CAGGGGAGGCGAACA 954s CAGGGGAGGCGAACA 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s GCGACCGCGTC 954s GCGACCGCGTC 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s AGGGGAGGCGAACAAAGG 954s AGGGGAGGCGAACAAAGG 954s Processing line... 954s TGCAGA 954s TGCAGA 954s Processing line... 954s Processing line... 954s GGGGA 954s GGGGA 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s TCGCAGCGGA 954s TCGCAGCGGA 954s Processing line... 954s Processing line... 954s AGGCGA 954s AGGCGA 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s GACC 954s GACC 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s GGGA 954s GGGA 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s GG 954s GG 954s Processing line... 954s ACAGCATAGTGCGACCG 954s ACAGCATAGTGCGACCG 954s Processing line... 954s AAGGGC 954s AAGGGC 954s Processing line... 954s CAGATGGGACAGGGGAGGCGAACAAA 954s CAGATGGGACAGGGGAGGCGAACAAA 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s TC 954s TC 954s Processing line... 954s Processing line... 954s Processing line... 954s CGG 954s CGG 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s GAGGC 954s GAGGC 954s Processing line... 954s AG 954s AG 954s /usr/bin/bowtie2 --large-index --score-min L,6.03035959442172,8.46511495836767 --rdg 28.0117598525247,2.32672796341212 --rfg 19.1893959544127 -D 21 --cp-ival 1 --cp-min 5 -q -p 4 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s ACG 954s ACG 954s Processing line... 954s Processing line... 954s CAGGGGAG 954s CAGGGGAG 954s Processing line... 954s Processing line... 954s Processing line... 954s GGGACAGGGGAGGCGAAC 954s GGGACAGGGGAGGCGAAC 954s --- Summary --- 954s Read 1 reference strings 954s Checked 21 alignments, 0 edits 954s --------------- 954s PASSED 954s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 954s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 954s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 954s Warning: skipping read '10' because it was < 2 characters long 954s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 954s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 954s Warning: skipping read '92' because it was < 2 characters long 954s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 954s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 954s Warning: skipping read '57' because it was < 2 characters long 954s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 954s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 954s 105 reads; of these: 954s 105 (100.00%) were unpaired; of these: 954s 84 (80.00%) aligned 0 times 954s 14 (13.33%) aligned exactly 1 time 954s 7 (6.67%) aligned >1 times 954s 20.00% overall alignment rate 954s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 954s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 954s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 954s Flattened IUPAC characters 954s Mutating sequence Sim.pm.1 954s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 954s Finished SNPs 954s Finished ref gaps 954s Finished read gaps 954s Mutating sequence Sim.pm.2 954s Introducing 12 SNPs, 1/0 ref/read gaps, and 0 rearrangements 954s Finished SNPs 954s Finished ref gaps 954s Finished read gaps 954s Mutated reference genome to subject genome 954s SNPs introduced: 15 954s Reference gaps introduced: 1 954s Read gaps introduced: 0 954s Rearrangements introduced: 0 954s Created read sampler 954s Sampling 131 reads 954s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 954s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 954s parsing sequence Sim.pm.1... 954s parsing sequence Sim.pm.2... 954s Parsed 110 reference bases 954s *** Run 27 of 100 954s /usr/bin/bowtie2 -i C,4.11216935586855 --gbar 3 --score-min L,1.7575423863675,3.19658873077018 -N 1 -L13 --local --large-index --cp-min 6 --mm --cp-ival 1 -r -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw 954s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #1 of read '2' because it was < 2 characters long 954s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #1 of read '36' because it was < 2 characters long 954s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #1 of read '51' because it was < 2 characters long 954s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #1 of read '55' because it was < 2 characters long 954s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #2 of read '65' because it was < 2 characters long 954s Warning: skipping mate #1 of read '88' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #1 of read '88' because it was < 2 characters long 954s Read 50 alignments... 954s Read 100 alignments... 954s Warning: skipping mate #2 of read '119' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #2 of read '119' because it was < 2 characters long 954s Read 150 alignments... 954s 131 reads; of these: 954s 131 (100.00%) were paired; of these: 954s 131 (100.00%) aligned concordantly 0 times 954s 0 (0.00%) aligned concordantly exactly 1 time 954s 0 (0.00%) aligned concordantly >1 times 954s ---- 954s 131 pairs aligned concordantly 0 times; of these: 954s 0 (0.00%) aligned discordantly 1 time 954s ---- 954s 131 pairs aligned 0 times concordantly or discordantly; of these: 954s 262 mates make up the pairs; of these: 954s 262 (100.00%) aligned 0 times 954s 0 (0.00%) aligned exactly 1 time 954s 0 (0.00%) aligned >1 times 954s 0.00% overall alignment rate 954s Read 200 alignments... 954s Read 250 alignments... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s 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line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s /usr/bin/bowtie2 -i C,4.11216935586855 --gbar 3 --score-min L,1.7575423863675,3.19658873077018 -N 1 -L13 --local --large-index --cp-min 6 --mm --cp-ival 1 -r -p 3 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s Processing line... 954s --- Summary --- 954s Read 1 reference strings 954s Checked 0 alignments, 0 edits 954s --------------- 954s PASSED 954s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 954s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #1 of read '2' because it was < 2 characters long 954s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #1 of read '51' because it was < 2 characters long 954s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #1 of read '55' because it was < 2 characters long 954s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #1 of read '36' because it was < 2 characters long 954s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #2 of read '65' because it was < 2 characters long 954s Warning: skipping mate #1 of read '88' because length (1) <= # seed mismatches (1) 954s Warning: skipping mate #1 of read '88' because it was < 2 characters long 955s Warning: skipping mate #2 of read '119' because length (1) <= # seed mismatches (1) 955s Warning: skipping mate #2 of read '119' because it was < 2 characters long 955s 131 reads; of these: 955s 131 (100.00%) were paired; of these: 955s 131 (100.00%) aligned concordantly 0 times 955s 0 (0.00%) aligned concordantly exactly 1 time 955s 0 (0.00%) aligned concordantly >1 times 955s ---- 955s 131 pairs aligned concordantly 0 times; of these: 955s 0 (0.00%) aligned discordantly 1 time 955s ---- 955s 131 pairs aligned 0 times concordantly or discordantly; of these: 955s 262 mates make up the pairs; of these: 955s 262 (100.00%) aligned 0 times 955s 0 (0.00%) aligned exactly 1 time 955s 0 (0.00%) aligned >1 times 955s 0.00% overall alignment rate 955s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 955s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 955s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 955s Flattened IUPAC characters 955s Mutating sequence Sim.pm.2 955s Introducing 4 SNPs, 1/1 ref/read gaps, and 0 rearrangements 955s Finished SNPs 955s Finished ref gaps 955s Finished read gaps 955s Mutating sequence Sim.pm.1 955s Introducing 3 SNPs, 1/0 ref/read gaps, and 2 rearrangements 955s Finished SNPs 955s Finished ref gaps 955s Finished read gaps 955s Mutated reference genome to subject genome 955s SNPs introduced: 7 955s Reference gaps introduced: 2 955s Read gaps introduced: 1 955s Rearrangements introduced: 2 955s Created read sampler 955s Sampling 26 reads 955s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 955s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 955s parsing sequence Sim.pm.1... 955s parsing sequence Sim.pm.2... 955s Parsed 110 reference bases 955s *** Run 28 of 100 955s /usr/bin/bowtie2 -N 1 -L21 --cp-ival 2 --cp-min 8 --np 1 --ma 11.6608883613607 --large-index --gbar 2 --score-min L,7.1618029716207,8.70041798126676 --rdg 18.2449585501205 --trim5 0 --mp 5.1622021746762,4.54756466324581 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 955s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (1) 955s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 26 reads; of these: 955s 26 (100.00%) were paired; of these: 955s 26 (100.00%) aligned concordantly 0 times 955s 0 (0.00%) aligned concordantly exactly 1 time 955s 0 (0.00%) aligned concordantly >1 times 955s ---- 955s 26 pairs aligned concordantly 0 times; of these: 955s 0 (0.00%) aligned discordantly 1 time 955s ---- 955s 26 pairs aligned 0 times concordantly or discordantly; of these: 955s 52 mates make up the pairs; of these: 955s 42 (80.77%) aligned 0 times 955s 8 (15.38%) aligned exactly 1 time 955s 2 (3.85%) aligned >1 times 955s 19.23% overall alignment rate 955s Read 50 alignments... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s GATG 955s GATG 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s GGCG 955s GGCG 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s GATGGGA 955s GATGGGA 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s TGGGACAGGGGAGGCGAA 955s TGGGACAGGGGAGGCGAA 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s ACAGGGGAGGCGAACAAAG 955s ACAGGGGAGGCGAACAAAG 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s AGATGGGA 955s AGATGGGA 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s AATGCAGATGGGACAGG 955s AATGCAGATGGGACAGG 955s Processing line... 955s Processing line... 955s GGGACGCACAGCATAGT 955s GGGACGCACAGCATAGT 955s /usr/bin/bowtie2 -N 1 -L21 --cp-ival 2 --cp-min 8 --np 1 --ma 11.6608883613607 --large-index --gbar 2 --score-min L,7.1618029716207,8.70041798126676 --rdg 18.2449585501205 --trim5 0 --mp 5.1622021746762,4.54756466324581 --qseq -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s CCT 955s CCT 955s Processing line... 955s Processing line... 955s GGAAG 955s GGAAG 955s Processing line... 955s --- Summary --- 955s Read 1 reference strings 955s Checked 10 alignments, 0 edits 955s --------------- 955s PASSED 955s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 955s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (1) 955s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 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 955s 26 reads; of these: 955s 26 (100.00%) were paired; of these: 955s 26 (100.00%) aligned concordantly 0 times 955s 0 (0.00%) aligned concordantly exactly 1 time 955s 0 (0.00%) aligned concordantly >1 times 955s ---- 955s 26 pairs aligned concordantly 0 times; of these: 955s 0 (0.00%) aligned discordantly 1 time 955s ---- 955s 26 pairs aligned 0 times concordantly or discordantly; of these: 955s 52 mates make up the pairs; of these: 955s 42 (80.77%) aligned 0 times 955s 8 (15.38%) aligned exactly 1 time 955s 2 (3.85%) aligned >1 times 955s 19.23% overall alignment rate 955s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 955s Flattened IUPAC characters 955s Mutating sequence Sim.pm.1 955s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 955s Finished SNPs 955s Finished ref gaps 955s Finished read gaps 955s Mutating sequence Sim.pm.2 955s Introducing 5 SNPs, 0/1 ref/read gaps, and 1 rearrangements 955s Finished SNPs 955s Finished ref gaps 955s Finished read gaps 955s Mutated reference genome to subject genome 955s SNPs introduced: 5 955s Reference gaps introduced: 1 955s Read gaps introduced: 2 955s Rearrangements introduced: 1 955s *** Run 29 of 100 955s /usr/bin/bowtie2 --cp-min 4 --cp-ival 1 --mm --local --mp 4.38594920458537,3.20684460996734 -a --rdg 31.7700861317373,1.94526795826283 --large-index --score-min L,9.54976508521011,1.79490503974582 --gbar 6 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 955s Created read sampler 955s Sampling 13 reads 955s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 955s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 955s parsing sequence Sim.pm.1... 955s parsing sequence Sim.pm.2... 955s Parsed 110 reference bases 955s 13 reads; of these: 955s 13 (100.00%) were unpaired; of these: 955s 13 (100.00%) aligned 0 times 955s 0 (0.00%) aligned exactly 1 time 955s 0 (0.00%) aligned >1 times 955s 0.00% overall alignment rate 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s Processing line... 955s --- Summary --- 955s /usr/bin/bowtie2 --cp-min 4 --cp-ival 1 --mm --local --mp 4.38594920458537,3.20684460996734 -a --rdg 31.7700861317373,1.94526795826283 --large-index --score-min L,9.54976508521011,1.79490503974582 --gbar 6 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 955s Read 1 reference strings 955s Checked 0 alignments, 0 edits 955s --------------- 955s PASSED 955s ALSO checking that bowtie2 and bowtie2-align match up 956s 13 reads; of these: 956s 13 (100.00%) were unpaired; of these: 956s 13 (100.00%) aligned 0 times 956s 0 (0.00%) aligned exactly 1 time 956s 0 (0.00%) aligned >1 times 956s 0.00% overall alignment rate 956s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 956s Flattened IUPAC characters 956s Mutating sequence Sim.pm.2 956s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 956s Finished SNPs 956s Finished ref gaps 956s Finished read gaps 956s Mutating sequence Sim.pm.1 956s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 956s Finished SNPs 956s Finished ref gaps 956s Finished read gaps 956s Mutated reference genome to subject genome 956s SNPs introduced: 15 956s Reference gaps introduced: 0 956s Read gaps introduced: 0 956s Rearrangements introduced: 0 956s Created read sampler 956s Sampling 66 reads 956s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 956s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 956s parsing sequence Sim.pm.1... 956s parsing sequence Sim.pm.2... 956s *** Run 30 of 100 956s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 4 --large-index --local --rdg 44.104797278488,19.7807765697902 --trim3 0 --np 1 --score-min L,9.61310576792527,5.22434310944246 --n-ceil 1.17360405705699,0.736888890683444 -i S,0.772671287728967,5.96308155165144 --rfg 26.3350066065209,10.3280436363461 --trim5 2 -f -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta 956s Parsed 110 reference bases 956s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 956s Warning: skipping read '13' because it was < 2 characters long 956s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 956s Warning: skipping read '15' because it was < 2 characters long 956s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 956s Warning: skipping read '24' because it was < 2 characters long 956s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 956s Warning: skipping read '32' because it was < 2 characters long 956s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 956s Warning: skipping read '38' because it was < 2 characters long 956s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 956s Warning: skipping read '56' because it was < 2 characters long 956s 66 reads; of these: 956s 66 (100.00%) were unpaired; of these: 956s 66 (100.00%) aligned 0 times 956s 0 (0.00%) aligned exactly 1 time 956s 0 (0.00%) aligned >1 times 956s 0.00% overall alignment rate 956s Read 50 alignments... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s --- Summary --- 956s Read 1 reference strings 956s Checked 0 alignments, 0 edits 956s --------------- 956s PASSED 956s Flattened IUPAC characters 956s Mutating sequence Sim.pm.2 956s Introducing 4 SNPs, 1/0 ref/read gaps, and 2 rearrangements 956s Finished SNPs 956s Finished ref gaps 956s Finished read gaps 956s Mutating sequence Sim.pm.1 956s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 956s Finished SNPs 956s Finished ref gaps 956s Finished read gaps 956s Mutated reference genome to subject genome 956s SNPs introduced: 5 956s Reference gaps introduced: 1 956s Read gaps introduced: 1 956s Rearrangements introduced: 3 956s Created read sampler 956s Sampling 121 reads 956s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 956s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 956s parsing sequence Sim.pm.1... 956s parsing sequence Sim.pm.2... 956s Parsed 110 reference bases 956s *** Run 31 of 100 956s /usr/bin/bowtie2 --rfg 10.9131147109972,11.4352439902703 --score-min L,9.46075699812004,8.06313189601815 -D 36 -R 2 --mp 9.81465692317385,1.60467592086524 -a --local --large-index --cp-min 3 --cp-ival 3 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 956s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 956s Warning: skipping mate #2 of read '27' because it was < 2 characters long 956s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 956s Warning: skipping mate #1 of read '53' because it was < 2 characters long 956s Read 50 alignments... 956s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 956s Warning: skipping mate #2 of read '103' because it was < 2 characters long 956s Read 100 alignments... 956s Read 150 alignments... 956s Read 200 alignments... 956s 121 reads; of these: 956s 121 (100.00%) were paired; of these: 956s 121 (100.00%) aligned concordantly 0 times 956s 0 (0.00%) aligned concordantly exactly 1 time 956s 0 (0.00%) aligned concordantly >1 times 956s ---- 956s 121 pairs aligned concordantly 0 times; of these: 956s 0 (0.00%) aligned discordantly 1 time 956s ---- 956s 121 pairs aligned 0 times concordantly or discordantly; of these: 956s 242 mates make up the pairs; of these: 956s 242 (100.00%) aligned 0 times 956s 0 (0.00%) aligned exactly 1 time 956s 0 (0.00%) aligned >1 times 956s 0.00% overall alignment rate 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s /usr/bin/bowtie2 --rfg 10.9131147109972,11.4352439902703 --score-min L,9.46075699812004,8.06313189601815 -D 36 -R 2 --mp 9.81465692317385,1.60467592086524 -a --local --large-index --cp-min 3 --cp-ival 3 -f -p 4 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s Processing line... 956s --- Summary --- 956s Read 1 reference strings 956s Checked 0 alignments, 0 edits 956s --------------- 956s PASSED 956s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 956s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 956s Warning: skipping mate #2 of read '27' because it was < 2 characters long 956s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 956s Warning: skipping mate #1 of read '53' because it was < 2 characters long 956s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 956s Warning: skipping mate #2 of read '103' because it was < 2 characters long 956s 121 reads; of these: 956s 121 (100.00%) were paired; of these: 956s 121 (100.00%) aligned concordantly 0 times 956s 0 (0.00%) aligned concordantly exactly 1 time 956s 0 (0.00%) aligned concordantly >1 times 956s ---- 956s 121 pairs aligned concordantly 0 times; of these: 956s 0 (0.00%) aligned discordantly 1 time 956s ---- 956s 121 pairs aligned 0 times concordantly or discordantly; of these: 956s 242 mates make up the pairs; of these: 956s 242 (100.00%) aligned 0 times 956s 0 (0.00%) aligned exactly 1 time 956s 0 (0.00%) aligned >1 times 956s 0.00% overall alignment rate 956s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 956s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 956s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 957s Flattened IUPAC characters 957s Mutating sequence Sim.pm.2 957s Introducing 17 SNPs, 0/2 ref/read gaps, and 1 rearrangements 957s Finished SNPs 957s Finished ref gaps 957s Finished read gaps 957s Mutating sequence Sim.pm.1 957s Introducing 0 SNPs, 1/2 ref/read gaps, and 0 rearrangements 957s Finished SNPs 957s Finished ref gaps 957s Finished read gaps 957s Mutated reference genome to subject genome 957s SNPs introduced: 17 957s Reference gaps introduced: 1 957s Read gaps introduced: 4 957s Rearrangements introduced: 1 957s Created read sampler 957s Sampling 43 reads 957s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 957s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 957s parsing sequence Sim.pm.1... 957s parsing sequence Sim.pm.2... 957s Parsed 110 reference bases 957s *** Run 32 of 100 957s /usr/bin/bowtie2 -N 0 --score-min L,7.23748229406122,3.4098430978305 --n-ceil 0.335073376298527,1.24673479258663 --cp-ival 2 --cp-min 2 --large-index --local -a -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 957s Warning: skipping mate #1 of read '26' because length (1) <= # seed mismatches (0) 957s Warning: skipping mate #1 of read '26' because it was < 2 characters long 957s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 957s Warning: skipping mate #1 of read '28' because it was < 2 characters long 957s 43 reads; of these: 957s 43 (100.00%) were paired; of these: 957s 43 (100.00%) aligned concordantly 0 times 957s 0 (0.00%) aligned concordantly exactly 1 time 957s 0 (0.00%) aligned concordantly >1 times 957s ---- 957s 43 pairs aligned concordantly 0 times; of these: 957s 0 (0.00%) aligned discordantly 1 time 957s ---- 957s 43 pairs aligned 0 times concordantly or discordantly; of these: 957s 86 mates make up the pairs; of these: 957s 86 (100.00%) aligned 0 times 957s 0 (0.00%) aligned exactly 1 time 957s 0 (0.00%) aligned >1 times 957s 0.00% overall alignment rate 957s Read 50 alignments... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s --- Summary --- 957s Read 1 reference strings 957s Checked 0 alignments, 0 edits 957s --------------- 957s PASSED 957s Flattened IUPAC characters 957s Mutating sequence Sim.pm.2 957s Introducing 12 SNPs, 1/0 ref/read gaps, and 3 rearrangements 957s Finished SNPs 957s Finished ref gaps 957s Finished read gaps 957s Mutating sequence Sim.pm.1 957s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 957s Finished SNPs 957s Finished ref gaps 957s Finished read gaps 957s Mutated reference genome to subject genome 957s SNPs introduced: 17 957s Reference gaps introduced: 2 957s Read gaps introduced: 1 957s Rearrangements introduced: 3 957s Created read sampler 957s Sampling 74 reads 957s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 957s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 957s parsing sequence Sim.pm.1... 957s parsing sequence Sim.pm.2... 957s Parsed 110 reference bases 957s *** Run 33 of 100 957s /usr/bin/bowtie2 --large-index --score-min L,7.73566727085585,9.44458930370868 --rdg 31.5483991483291 --mp 5.62335259932325,3.18967475840932 --local --rfg 43.2761310923245 --cp-ival 1 --cp-min 2 --np 3 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 957s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 957s Warning: skipping read '2' because it was < 2 characters long 957s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 957s Warning: skipping read '29' because it was < 2 characters long 957s 74 reads; of these: 957s 74 (100.00%) were unpaired; of these: 957s 74 (100.00%) aligned 0 times 957s 0 (0.00%) aligned exactly 1 time 957s 0 (0.00%) aligned >1 times 957s 0.00% overall alignment rate 957s Read 50 alignments... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s --- Summary --- 957s Read 1 reference strings 957s Checked 0 alignments, 0 edits 957s --------------- 957s PASSED 957s Flattened IUPAC characters 957s Mutating sequence Sim.pm.2 957s *** Run 34 of 100 957s /usr/bin/bowtie2 --cp-min 2 -N 0 -L27 -D 36 --cp-ival 1 --rdg 15.5736763280642,4.73770261868123 --trim5 4 -i S,0.691417692122284,4.28540109761948 --large-index --score-min L,1.48981212993806,6.33980603976339 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 957s Introducing 8 SNPs, 2/2 ref/read gaps, and 0 rearrangements 957s Finished SNPs 957s Finished ref gaps 957s Finished read gaps 957s Mutating sequence Sim.pm.1 957s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 957s Finished SNPs 957s Finished ref gaps 957s Finished read gaps 957s Mutated reference genome to subject genome 957s SNPs introduced: 13 957s Reference gaps introduced: 2 957s Read gaps introduced: 2 957s Rearrangements introduced: 1 957s Created read sampler 957s Sampling 18 reads 957s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 957s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 957s parsing sequence Sim.pm.1... 957s parsing sequence Sim.pm.2... 957s Parsed 110 reference bases 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 957s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 957s Warning: skipping mate #1 of read '1' because it was < 2 characters long 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 957s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 957s Warning: skipping mate #1 of read '13' because it was < 2 characters long 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 957s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 957s 18 reads; of these: 957s 15 (83.33%) were paired; of these: 957s 15 (100.00%) aligned concordantly 0 times 957s 0 (0.00%) aligned concordantly exactly 1 time 957s 0 (0.00%) aligned concordantly >1 times 957s ---- 957s 15 pairs aligned concordantly 0 times; of these: 957s 0 (0.00%) aligned discordantly 1 time 957s ---- 957s 15 pairs aligned 0 times concordantly or discordantly; of these: 957s 30 mates make up the pairs; of these: 957s 24 (80.00%) aligned 0 times 957s 5 (16.67%) aligned exactly 1 time 957s 1 (3.33%) aligned >1 times 957s 3 (16.67%) were unpaired; of these: 957s 3 (100.00%) aligned 0 times 957s 0 (0.00%) aligned exactly 1 time 957s 0 (0.00%) aligned >1 times 957s 18.18% overall alignment rate 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s CGAAT 957s CGAAT 957s Processing line... 957s Processing line... 957s GCT 957s GCT 957s Processing line... 957s GGCG 957s GGCG 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s GATGGGACAGGGGAGGCGAAC 957s GATGGGACAGGGGAGGCGAAC 957s Processing line... 957s Processing line... 957s CCTCGC 957s CCTCGC 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s Processing line... 957s AGATGGG 957s AGATGGG 957s Processing line... 957s --- Summary --- 957s Read 1 reference strings 957s Checked 6 alignments, 0 edits 957s --------------- 957s PASSED 957s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 957s /usr/bin/bowtie2 --cp-min 2 -N 0 -L27 -D 36 --cp-ival 1 --rdg 15.5736763280642,4.73770261868123 --trim5 4 -i S,0.691417692122284,4.28540109761948 --large-index --score-min L,1.48981212993806,6.33980603976339 -f -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 958s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #1 of read '1' because it was < 2 characters long 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 958s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 958s Warning: skipping mate #1 of read '13' because it was < 2 characters long 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 958s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 958s 18 reads; of these: 958s 15 (83.33%) were paired; of these: 958s 15 (100.00%) aligned concordantly 0 times 958s 0 (0.00%) aligned concordantly exactly 1 time 958s 0 (0.00%) aligned concordantly >1 times 958s ---- 958s 15 pairs aligned concordantly 0 times; of these: 958s 0 (0.00%) aligned discordantly 1 time 958s ---- 958s 15 pairs aligned 0 times concordantly or discordantly; of these: 958s 30 mates make up the pairs; of these: 958s 24 (80.00%) aligned 0 times 958s 5 (16.67%) aligned exactly 1 time 958s 1 (3.33%) aligned >1 times 958s 3 (16.67%) were unpaired; of these: 958s 3 (100.00%) aligned 0 times 958s 0 (0.00%) aligned exactly 1 time 958s 0 (0.00%) aligned >1 times 958s 18.18% overall alignment rate 958s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 958s Flattened IUPAC characters 958s Mutating sequence Sim.pm.1 958s Introducing 8 SNPs, 0/0 ref/read gaps, and 3 rearrangements 958s Finished SNPs 958s Finished ref gaps 958s Finished read gaps 958s Mutating sequence Sim.pm.2 958s Introducing 19 SNPs, 0/1 ref/read gaps, and 2 rearrangements 958s Finished SNPs 958s Finished ref gaps 958s Finished read gaps 958s Mutated reference genome to subject genome 958s SNPs introduced: 27 958s Reference gaps introduced: 0 958s Read gaps introduced: 1 958s Rearrangements introduced: 5 958s Created read sampler 958s Sampling 101 reads 958s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 958s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 958s parsing sequence Sim.pm.1... 958s parsing sequence Sim.pm.2... 958s Parsed 110 reference bases 958s *** Run 35 of 100 958s /usr/bin/bowtie2 --score-min L,1.24085842700348,8.94382116674669 --large-index -i S,1.86954361987822 --rfg 42.5496377044913 --local --mp 8.66805626907609,6.56160325544713 -R 3 --cp-ival 2 --nofw --cp-min 3 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 958s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 958s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 958s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 958s Read 50 alignments... 958s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 958s Warning: skipping mate #2 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 958s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 958s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 958s Read 100 alignments... 958s Read 150 alignments... 958s 101 reads; of these: 958s 101 (100.00%) were paired; of these: 958s 101 (100.00%) aligned concordantly 0 times 958s 0 (0.00%) aligned concordantly exactly 1 time 958s 0 (0.00%) aligned concordantly >1 times 958s ---- 958s 101 pairs aligned concordantly 0 times; of these: 958s 0 (0.00%) aligned discordantly 1 time 958s ---- 958s 101 pairs aligned 0 times concordantly or discordantly; of these: 958s 202 mates make up the pairs; of these: 958s 202 (100.00%) aligned 0 times 958s 0 (0.00%) aligned exactly 1 time 958s 0 (0.00%) aligned >1 times 958s 0.00% overall alignment rate 958s Read 200 alignments... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s Processing line... 958s --- Summary --- 958s Read 1 reference strings 958s Checked 0 alignments, 0 edits 958s --------------- 958s PASSED 958s ALSO checking that bowtie2 and bowtie2-align match up 958s /usr/bin/bowtie2 --score-min L,1.24085842700348,8.94382116674669 --large-index -i S,1.86954361987822 --rfg 42.5496377044913 --local --mp 8.66805626907609,6.56160325544713 -R 3 --cp-ival 2 --nofw --cp-min 3 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 958s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 958s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 958s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 958s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 958s Warning: skipping mate #2 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 958s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 958s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 958s 101 reads; of these: 958s 101 (100.00%) were paired; of these: 958s 101 (100.00%) aligned concordantly 0 times 958s 0 (0.00%) aligned concordantly exactly 1 time 958s 0 (0.00%) aligned concordantly >1 times 958s ---- 958s 101 pairs aligned concordantly 0 times; of these: 958s 0 (0.00%) aligned discordantly 1 time 958s ---- 958s 101 pairs aligned 0 times concordantly or discordantly; of these: 958s 202 mates make up the pairs; of these: 958s 202 (100.00%) aligned 0 times 958s 0 (0.00%) aligned exactly 1 time 958s 0 (0.00%) aligned >1 times 958s 0.00% overall alignment rate 958s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 958s /usr/bin/bowtie2 --score-min L,1.24085842700348,8.94382116674669 --large-index -i S,1.86954361987822 --rfg 42.5496377044913 --local --mp 8.66805626907609,6.56160325544713 -R 3 --cp-ival 2 --nofw --cp-min 3 --qseq -p 4 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 958s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 958s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 958s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 958s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 959s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 959s Warning: skipping mate #2 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 959s Warning: skipping mate #2 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 959s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 959s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 959s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 959s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 959s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 959s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 959s 101 reads; of these: 959s 101 (100.00%) were paired; of these: 959s 101 (100.00%) aligned concordantly 0 times 959s 0 (0.00%) aligned concordantly exactly 1 time 959s 0 (0.00%) aligned concordantly >1 times 959s ---- 959s 101 pairs aligned concordantly 0 times; of these: 959s 0 (0.00%) aligned discordantly 1 time 959s ---- 959s 101 pairs aligned 0 times concordantly or discordantly; of these: 959s 202 mates make up the pairs; of these: 959s 202 (100.00%) aligned 0 times 959s 0 (0.00%) aligned exactly 1 time 959s 0 (0.00%) aligned >1 times 959s 0.00% overall alignment rate 959s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 959s Flattened IUPAC characters 959s Mutating sequence Sim.pm.2 959s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 959s Finished SNPs 959s Finished ref gaps 959s Finished read gaps 959s Mutating sequence Sim.pm.1 959s Introducing 10 SNPs, 2/0 ref/read gaps, and 0 rearrangements 959s Finished SNPs 959s Finished ref gaps 959s Finished read gaps 959s Mutated reference genome to subject genome 959s SNPs introduced: 16 959s Reference gaps introduced: 2 959s Read gaps introduced: 0 959s Rearrangements introduced: 0 959s Created read sampler 959s Sampling 139 reads 959s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 959s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 959s parsing sequence Sim.pm.1... 959s parsing sequence Sim.pm.2... 959s Parsed 110 reference bases 959s *** Run 36 of 100 959s /usr/bin/bowtie2 --rfg 8.10771087564315,18.5330410452133 -i C,0.46510820022514 --score-min L,3.90544446183498,3.14084186822714 --norc --trim3 7 -k 4 --large-index --cp-min 3 --mm --cp-ival 2 -r -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw 959s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 959s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '6' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 959s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '7' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 959s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 959s Warning: skipping read '11' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 959s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '17' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 959s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '18' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 959s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 959s Warning: skipping read '21' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 959s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '29' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 959s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '39' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 959s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '41' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 959s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '58' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 959s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '63' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 959s Read 50 alignments... 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 959s Read 100 alignments... 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 959s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '67' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 959s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '73' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 959s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 959s Warning: skipping mate #2 of read '80' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 959s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '91' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 959s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '99' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 959s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 959s Warning: skipping read '100' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 959s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '104' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 959s Warning: skipping mate #1 of read '110' because length (1) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '110' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 959s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '116' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 959s Read 150 alignments... 959s Read 200 alignments... 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 959s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '127' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 959s Warning: skipping mate #1 of read '131' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '131' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 959s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '132' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 959s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '134' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 959s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '136' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 959s 139 reads; of these: 959s 120 (86.33%) were paired; of these: 959s 120 (100.00%) aligned concordantly 0 times 959s 0 (0.00%) aligned concordantly exactly 1 time 959s 0 (0.00%) aligned concordantly >1 times 959s ---- 959s 120 pairs aligned concordantly 0 times; of these: 959s 0 (0.00%) aligned discordantly 1 time 959s ---- 959s 120 pairs aligned 0 times concordantly or discordantly; of these: 959s 240 mates make up the pairs; of these: 959s 224 (93.33%) aligned 0 times 959s 12 (5.00%) aligned exactly 1 time 959s 4 (1.67%) aligned >1 times 959s 19 (13.67%) were unpaired; of these: 959s 19 (100.00%) aligned 0 times 959s 0 (0.00%) aligned exactly 1 time 959s 0 (0.00%) aligned >1 times 959s 6.18% overall alignment rate 959s Read 250 alignments... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s ATGCAGATGGGACAGG 959s ATGCAGATGGGACAGG 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s TCGCAGCGGAAGC 959s TCGCAGCGGAAGC 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s GATG 959s GATG 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s CGAATGCAGATGG 959s CGAATGCAGATGG 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s AAG 959s AAG 959s Processing line... 959s AAG 959s AAG 959s Processing line... 959s AAG 959s AAG 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s GGGACA 959s GGGACA 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s GAGGCGAA 959s GAGGCGAA 959s Processing line... 959s Processing line... 959s CAG 959s CAG 959s Processing line... 959s CAG 959s CAG 959s Processing line... 959s CAG 959s CAG 959s Processing line... 959s CAG 959s CAG 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s GCAGATGGGACAGGGGAGGCGAACAAAGGG 959s GCAGATGGGACAGGGGAGGCGAACAAAGGG 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s CCTCGCAGCGGAA 959s CCTCGCAGCGGAA 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s GCATAGT 959s GCATAGT 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s CAGG 959s CAGG 959s Processing line... 959s CAGG 959s CAGG 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s CAGGGGAGGCGAACAAAG 959s CAGGGGAGGCGAACAAAG 959s /usr/bin/bowtie2 --rfg 8.10771087564315,18.5330410452133 -i C,0.46510820022514 --score-min L,3.90544446183498,3.14084186822714 --norc --trim3 7 -k 4 --large-index --cp-min 3 --mm --cp-ival 2 -r -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 959s Processing line... 959s Processing line... 959s TGGGA 959s TGGGA 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s AGGGCCTCGCAGCGGAAG 959s AGGGCCTCGCAGCGGAAG 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s Processing line... 959s AT 959s AT 959s Processing line... 959s AT 959s AT 959s Processing line... 959s AT 959s AT 959s Processing line... 959s AT 959s AT 959s Processing line... 959s --- Summary --- 959s Read 1 reference strings 959s Checked 25 alignments, 0 edits 959s --------------- 959s PASSED 959s ALSO checking that bowtie2 and bowtie2-align match up 959s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 959s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '6' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 959s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '7' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 959s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 959s Warning: skipping read '11' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 959s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '17' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 959s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '18' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 959s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 959s Warning: skipping read '21' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 959s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '29' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 959s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '39' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 959s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '41' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 959s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '58' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 959s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '63' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 959s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '67' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 959s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '73' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 959s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 959s Warning: skipping mate #2 of read '80' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 959s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '91' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 959s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '99' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 959s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 959s Warning: skipping read '100' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 959s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '104' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 959s Warning: skipping mate #1 of read '110' because length (1) <= # seed mismatches (0) 959s Warning: skipping mate #1 of read '110' because it was < 2 characters long 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 959s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 960s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '116' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 960s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '127' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 960s Warning: skipping mate #1 of read '131' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '131' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 960s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '132' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 960s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '134' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 960s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '136' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 960s 139 reads; of these: 960s 120 (86.33%) were paired; of these: 960s 120 (100.00%) aligned concordantly 0 times 960s 0 (0.00%) aligned concordantly exactly 1 time 960s 0 (0.00%) aligned concordantly >1 times 960s ---- 960s 120 pairs aligned concordantly 0 times; of these: 960s 0 (0.00%) aligned discordantly 1 time 960s ---- 960s 120 pairs aligned 0 times concordantly or discordantly; of these: 960s 240 mates make up the pairs; of these: 960s 224 (93.33%) aligned 0 times 960s 12 (5.00%) aligned exactly 1 time 960s 4 (1.67%) aligned >1 times 960s 19 (13.67%) were unpaired; of these: 960s 19 (100.00%) aligned 0 times 960s 0 (0.00%) aligned exactly 1 time 960s 0 (0.00%) aligned >1 times 960s 6.18% overall alignment rate 960s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 960s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 960s /usr/bin/bowtie2 --rfg 8.10771087564315,18.5330410452133 -i C,0.46510820022514 --score-min L,3.90544446183498,3.14084186822714 --norc --trim3 7 -k 4 --large-index --cp-min 3 --mm --cp-ival 2 -r -p 4 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 960s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 960s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '17' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 960s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '6' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 960s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '18' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 960s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 960s Warning: skipping read '21' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 960s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '29' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 960s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '39' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 960s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '41' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 960s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '67' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 960s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '7' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 960s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '73' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 960s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 960s Warning: skipping mate #2 of read '80' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 960s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '58' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 960s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '63' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 960s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 960s Warning: skipping read '11' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 960s Warning: skipping mate #1 of read '131' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '131' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 960s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '116' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 960s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '127' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 960s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '91' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 960s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '99' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 960s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 960s Warning: skipping read '100' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 960s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '104' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 960s Warning: skipping mate #1 of read '110' because length (1) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '110' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 960s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '132' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 960s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '134' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 960s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 960s Warning: skipping mate #1 of read '136' because it was < 2 characters long 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 960s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 960s 139 reads; of these: 960s 120 (86.33%) were paired; of these: 960s 120 (100.00%) aligned concordantly 0 times 960s 0 (0.00%) aligned concordantly exactly 1 time 960s 0 (0.00%) aligned concordantly >1 times 960s ---- 960s 120 pairs aligned concordantly 0 times; of these: 960s 0 (0.00%) aligned discordantly 1 time 960s ---- 960s 120 pairs aligned 0 times concordantly or discordantly; of these: 960s 240 mates make up the pairs; of these: 960s 224 (93.33%) aligned 0 times 960s 12 (5.00%) aligned exactly 1 time 960s 4 (1.67%) aligned >1 times 960s 19 (13.67%) were unpaired; of these: 960s 19 (100.00%) aligned 0 times 960s 0 (0.00%) aligned exactly 1 time 960s 0 (0.00%) aligned >1 times 960s 6.18% overall alignment rate 960s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 960s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 960s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 960s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 960s /usr/bin/bowtie2 --rfg 8.10771087564315,18.5330410452133 -i C,0.46510820022514 --score-min L,3.90544446183498,3.14084186822714 --norc --trim3 7 -k 4 --large-index --cp-min 3 --mm --cp-ival 2 -r -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 961s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 961s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '17' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 961s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '18' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 961s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '6' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 961s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 961s Warning: skipping read '21' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 961s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '29' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 961s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '39' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 961s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '41' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 961s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '7' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 961s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '58' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 961s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '63' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 961s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '67' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 961s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '73' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 961s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 961s Warning: skipping read '11' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 961s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 961s Warning: skipping mate #2 of read '80' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 961s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '99' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 961s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 961s Warning: skipping read '100' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 961s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '104' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 961s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '91' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 961s Warning: skipping mate #1 of read '110' because length (1) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '110' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 961s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '116' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 961s Warning: skipping mate #1 of read '131' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '131' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 961s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '127' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 961s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '132' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 961s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '134' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 961s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '136' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 961s 139 reads; of these: 961s 120 (86.33%) were paired; of these: 961s 120 (100.00%) aligned concordantly 0 times 961s 0 (0.00%) aligned concordantly exactly 1 time 961s 0 (0.00%) aligned concordantly >1 times 961s ---- 961s 120 pairs aligned concordantly 0 times; of these: 961s 0 (0.00%) aligned discordantly 1 time 961s ---- 961s 120 pairs aligned 0 times concordantly or discordantly; of these: 961s 240 mates make up the pairs; of these: 961s 224 (93.33%) aligned 0 times 961s 12 (5.00%) aligned exactly 1 time 961s 4 (1.67%) aligned >1 times 961s 19 (13.67%) were unpaired; of these: 961s 19 (100.00%) aligned 0 times 961s 0 (0.00%) aligned exactly 1 time 961s 0 (0.00%) aligned >1 times 961s 6.18% overall alignment rate 961s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 961s Flattened IUPAC characters 961s Mutating sequence Sim.pm.2 961s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 961s Finished SNPs 961s Finished ref gaps 961s Finished read gaps 961s Mutating sequence Sim.pm.1 961s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 961s Finished SNPs 961s Finished ref gaps 961s Finished read gaps 961s Mutated reference genome to subject genome 961s SNPs introduced: 12 961s Reference gaps introduced: 1 961s Read gaps introduced: 1 961s Rearrangements introduced: 0 961s Created read sampler 961s Sampling 124 reads 961s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 961s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 961s parsing sequence Sim.pm.1... 961s parsing sequence Sim.pm.2... 961s Parsed 110 reference bases 961s *** Run 37 of 100 961s /usr/bin/bowtie2 --score-min L,4.97632619318912,8.98876757782197 --large-index -i S,2.05615699932601,6.03908948615315 --rfg 16.6812760140321 --rdg 27.9097141014997 --mm -D 24 --cp-ival 1 --cp-min 6 -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 961s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '21' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 961s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 961s Warning: skipping mate #2 of read '26' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 961s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 961s Warning: skipping mate #1 of read '53' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 961s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 961s Warning: skipping mate #2 of read '65' because it was < 2 characters long 961s Read 50 alignments... 961s Read 100 alignments... 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 961s Warning: skipping mate #2 of read '112' because length (1) <= # seed mismatches (0) 961s Warning: skipping mate #2 of read '112' because it was < 2 characters long 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 961s Read 150 alignments... 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 961s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 961s Read 200 alignments... 961s 124 reads; of these: 961s 124 (100.00%) were paired; of these: 961s 123 (99.19%) aligned concordantly 0 times 961s 1 (0.81%) aligned concordantly exactly 1 time 961s 0 (0.00%) aligned concordantly >1 times 961s ---- 961s 123 pairs aligned concordantly 0 times; of these: 961s 2 (1.63%) aligned discordantly 1 time 961s ---- 961s 121 pairs aligned 0 times concordantly or discordantly; of these: 961s 242 mates make up the pairs; of these: 961s 209 (86.36%) aligned 0 times 961s 23 (9.50%) aligned exactly 1 time 961s 10 (4.13%) aligned >1 times 961s 15.73% overall alignment rate 961s Read 250 alignments... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s ATGCA 961s ATGCA 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s TGCAGATGGGACA 961s TGCAGATGGGACA 961s Processing line... 961s AGATGGGACAGGGGAGGCGAACAAAG 961s AGATGGGACAGGGGAGGCGAACAAAG 961s Processing line... 961s CAGATGGGACAGGGGAGGCGAACAAAGG 961s CAGATGGGACAGGGGAGGCGAACAAAGG 961s Processing line... 961s Processing line... 961s GCAGATGGGACAGGGGAGGCGAACA 961s GCAGATGGGACAGGGGAGGCGAACA 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s AC 961s AC 961s Processing line... 961s Processing line... 961s GGCGA 961s GGCGA 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s TGTCC 961s TGTCC 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s CCAGGGACGCACAGCATAGTGCGACC 961s CCAGGGACGCACAGCATAGTGCGACC 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s AAG 961s AAG 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GC 961s GC 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s CT 961s CT 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s TGGGACAGGGGAGGCGAA 961s TGGGACAGGGGAGGCGAA 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GAATGCAGATGGGACAGGGGAGGCGAACAAAGGGC 961s GAATGCAGATGGGACAGGGGAGGCGAACAAAGGGC 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GAATGCAGATGGGACAGGGGAGGCGAACAAAGGG 961s GAATGCAGATGGGACAGGGGAGGCGAACAAAGGG 961s Processing line... 961s Processing line... 961s GACAGGGGAGGC 961s GACAGGGGAGGC 961s Processing line... 961s Processing line... 961s AGGGACGC 961s AGGGACGC 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GTCCAGGGACG 961s GTCCAGGGACG 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s CAG 961s CAG 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GGACAGGGG 961s GGACAGGGG 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GGGGAGG 961s GGGGAGG 961s Processing line... 961s Processing line... 961s GAACAAAGGGCCTCG 961s GAACAAAGGGCCTCG 961s Processing line... 961s CGGA 961s CGGA 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s /usr/bin/bowtie2 --score-min L,4.97632619318912,8.98876757782197 --large-index -i S,2.05615699932601,6.03908948615315 --rfg 16.6812760140321 --rdg 27.9097141014997 --mm -D 24 --cp-ival 1 --cp-min 6 -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s TC 961s TC 961s Processing line... 961s Processing line... 961s AGGGGAGGCGAACAAAGGG 961s AGGGGAGGCGAACAAAGGG 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GGCG 961s GGCG 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GGA 961s GGA 961s Processing line... 961s Processing line... 961s GACAGGGGAGGCGAACAAA 961s GACAGGGGAGGCGAACAAA 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GATGGGACAGGGGAGGCGAACAAAGGGCCTCGC 961s GATGGGACAGGGGAGGCGAACAAAGGGCCTCGC 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s ACC 961s ACC 961s Processing line... 961s Processing line... 961s CA 961s CA 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s ATGCAGATGGGACAGG 961s ATGCAGATGGGACAGG 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s ATGCAGATGGGACAGGGG 961s ATGCAGATGGGACAGGGG 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GC 961s GC 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s AAGGGCCTCGCAG 961s AAGGGCCTCGCAG 961s Processing line... 961s AGGCGAACAAAGGGC 961s AGGCGAACAAAGGGC 961s Processing line... 961s Processing line... 961s Processing line... 961s CGCAGCGG 961s CGCAGCGG 961s Processing line... 961s Processing line... 961s AGGGGAGG 961s AGGGGAGG 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s GCGAACAAAGGG 961s GCGAACAAAGGG 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s Processing line... 961s --- Summary --- 961s Read 1 reference strings 961s Checked 39 alignments, 0 edits 961s --------------- 961s PASSED 961s ALSO checking that bowtie2 and bowtie2-align match up 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 962s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '21' because it was < 2 characters long 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 962s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #2 of read '26' because it was < 2 characters long 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 962s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '53' because it was < 2 characters long 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 962s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #2 of read '65' because it was < 2 characters long 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 962s Warning: skipping mate #2 of read '112' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #2 of read '112' because it was < 2 characters long 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 962s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 962s 124 reads; of these: 962s 124 (100.00%) were paired; of these: 962s 123 (99.19%) aligned concordantly 0 times 962s 1 (0.81%) aligned concordantly exactly 1 time 962s 0 (0.00%) aligned concordantly >1 times 962s ---- 962s 123 pairs aligned concordantly 0 times; of these: 962s 2 (1.63%) aligned discordantly 1 time 962s ---- 962s 121 pairs aligned 0 times concordantly or discordantly; of these: 962s 242 mates make up the pairs; of these: 962s 209 (86.36%) aligned 0 times 962s 23 (9.50%) aligned exactly 1 time 962s 10 (4.13%) aligned >1 times 962s 15.73% overall alignment rate 962s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 962s Flattened IUPAC characters 962s Mutating sequence Sim.pm.2 962s Introducing 11 SNPs, 0/0 ref/read gaps, and 1 rearrangements 962s Finished SNPs 962s Finished ref gaps 962s Finished read gaps 962s Mutating sequence Sim.pm.1 962s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 962s Finished SNPs 962s Finished ref gaps 962s Finished read gaps 962s Mutated reference genome to subject genome 962s SNPs introduced: 19 962s Reference gaps introduced: 0 962s Read gaps introduced: 0 962s Rearrangements introduced: 2 962s Created read sampler 962s Sampling 48 reads 962s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 962s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 962s parsing sequence Sim.pm.1... 962s parsing sequence Sim.pm.2... 962s Parsed 110 reference bases 962s *** Run 38 of 100 962s /usr/bin/bowtie2 --score-min L,9.96188484447087,9.45008204889343 --rfg 29.9196384326412 -i L,0.244325408603838 --trim5 0 --norc --large-index --local --rdg 29.5679631402143,9.57014729104122 --mp 4.45816047254188,3.27732865259654 --trim3 9 --mm --cp-ival 1 --cp-min 11 -r -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw 962s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '5' because it was < 2 characters long 962s Warning: skipping mate #2 of read '5' because it was < 2 characters long 962s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 962s Warning: skipping read '9' because it was < 2 characters long 962s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '19' because it was < 2 characters long 962s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '28' because it was < 2 characters long 962s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '36' because it was < 2 characters long 962s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '38' because it was < 2 characters long 962s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '44' because it was < 2 characters long 962s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '45' because it was < 2 characters long 962s 48 reads; of these: 962s 40 (83.33%) were paired; of these: 962s 40 (100.00%) aligned concordantly 0 times 962s 0 (0.00%) aligned concordantly exactly 1 time 962s 0 (0.00%) aligned concordantly >1 times 962s ---- 962s 40 pairs aligned concordantly 0 times; of these: 962s 0 (0.00%) aligned discordantly 1 time 962s ---- 962s 40 pairs aligned 0 times concordantly or discordantly; of these: 962s 80 mates make up the pairs; of these: 962s 80 (100.00%) aligned 0 times 962s 0 (0.00%) aligned exactly 1 time 962s 0 (0.00%) aligned >1 times 962s 8 (16.67%) were unpaired; of these: 962s 8 (100.00%) aligned 0 times 962s 0 (0.00%) aligned exactly 1 time 962s 0 (0.00%) aligned >1 times 962s 0.00% overall alignment rate 962s Read 50 alignments... 962s Processing line... 962s /usr/bin/bowtie2 --score-min L,9.96188484447087,9.45008204889343 --rfg 29.9196384326412 -i L,0.244325408603838 --trim5 0 --norc --large-index --local --rdg 29.5679631402143,9.57014729104122 --mp 4.45816047254188,3.27732865259654 --trim3 9 --mm --cp-ival 1 --cp-min 11 -r -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s Processing line... 962s --- Summary --- 962s Read 1 reference strings 962s Checked 0 alignments, 0 edits 962s --------------- 962s PASSED 962s ALSO checking that bowtie2 and bowtie2-align match up 962s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '5' because it was < 2 characters long 962s Warning: skipping mate #2 of read '5' because it was < 2 characters long 962s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 962s Warning: skipping read '9' because it was < 2 characters long 962s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '19' because it was < 2 characters long 962s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '28' because it was < 2 characters long 962s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '36' because it was < 2 characters long 962s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '38' because it was < 2 characters long 962s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '44' because it was < 2 characters long 962s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '45' because it was < 2 characters long 962s 48 reads; of these: 962s 40 (83.33%) were paired; of these: 962s 40 (100.00%) aligned concordantly 0 times 962s 0 (0.00%) aligned concordantly exactly 1 time 962s 0 (0.00%) aligned concordantly >1 times 962s ---- 962s 40 pairs aligned concordantly 0 times; of these: 962s 0 (0.00%) aligned discordantly 1 time 962s ---- 962s 40 pairs aligned 0 times concordantly or discordantly; of these: 962s 80 mates make up the pairs; of these: 962s 80 (100.00%) aligned 0 times 962s 0 (0.00%) aligned exactly 1 time 962s 0 (0.00%) aligned >1 times 962s 8 (16.67%) were unpaired; of these: 962s 8 (100.00%) aligned 0 times 962s 0 (0.00%) aligned exactly 1 time 962s 0 (0.00%) aligned >1 times 962s 0.00% overall alignment rate 962s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 962s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 962s /usr/bin/bowtie2 --score-min L,9.96188484447087,9.45008204889343 --rfg 29.9196384326412 -i L,0.244325408603838 --trim5 0 --norc --large-index --local --rdg 29.5679631402143,9.57014729104122 --mp 4.45816047254188,3.27732865259654 --trim3 9 --mm --cp-ival 1 --cp-min 11 -r -p 4 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 962s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '5' because it was < 2 characters long 962s Warning: skipping mate #2 of read '5' because it was < 2 characters long 962s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 962s Warning: skipping read '9' because it was < 2 characters long 962s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '19' because it was < 2 characters long 962s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '28' because it was < 2 characters long 962s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '36' because it was < 2 characters long 962s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '38' because it was < 2 characters long 962s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '44' because it was < 2 characters long 962s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 962s Warning: skipping mate #1 of read '45' because it was < 2 characters long 962s 48 reads; of these: 962s 40 (83.33%) were paired; of these: 962s 40 (100.00%) aligned concordantly 0 times 962s 0 (0.00%) aligned concordantly exactly 1 time 962s 0 (0.00%) aligned concordantly >1 times 962s ---- 962s 40 pairs aligned concordantly 0 times; of these: 962s 0 (0.00%) aligned discordantly 1 time 962s ---- 962s 40 pairs aligned 0 times concordantly or discordantly; of these: 962s 80 mates make up the pairs; of these: 962s 80 (100.00%) aligned 0 times 962s 0 (0.00%) aligned exactly 1 time 962s 0 (0.00%) aligned >1 times 962s 8 (16.67%) were unpaired; of these: 962s 8 (100.00%) aligned 0 times 962s 0 (0.00%) aligned exactly 1 time 962s 0 (0.00%) aligned >1 times 962s 0.00% overall alignment rate 962s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 962s Flattened IUPAC characters 962s Mutating sequence Sim.pm.2 962s Introducing 10 SNPs, 0/0 ref/read gaps, and 3 rearrangements 962s Finished SNPs 962s Finished ref gaps 962s Finished read gaps 962s Mutating sequence Sim.pm.1 962s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 962s Finished SNPs 962s Finished ref gaps 962s Finished read gaps 962s Mutated reference genome to subject genome 962s SNPs introduced: 10 962s Reference gaps introduced: 0 962s Read gaps introduced: 0 962s Rearrangements introduced: 3 962s Created read sampler 962s Sampling 122 reads 962s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 962s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 962s parsing sequence Sim.pm.1... 962s parsing sequence Sim.pm.2... 962s Parsed 110 reference bases 962s *** Run 39 of 100 962s /usr/bin/bowtie2 --score-min L,6.74256623867812,6.60348650407808 --trim5 7 -R 2 -D 16 --np 4 --nofw --ma 38.5561041977577 --large-index --rdg 11.3990264567161 --mp 8.11730078559861,2.32332866801086 --trim3 2 --cp-ival 1 --cp-min 3 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 962s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 963s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 963s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '2' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 963s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '11' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 963s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '16' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 963s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 963s Warning: skipping read '18' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 963s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '22' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 963s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '27' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 963s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '30' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 963s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '31' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 963s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '34' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 963s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '35' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 963s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '37' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 963s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '43' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 963s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '47' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 963s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '52' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 963s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '55' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 963s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '66' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 963s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '67' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 963s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '70' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 963s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '71' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 963s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '72' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 963s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '84' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 963s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '91' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 963s Warning: skipping read '97' because length (1) <= # seed mismatches (0) 963s Warning: skipping read '97' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 963s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '101' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 963s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '104' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 963s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '106' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 963s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '108' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 963s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '121' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 963s 122 reads; of these: 963s 122 (100.00%) were unpaired; of these: 963s 108 (88.52%) aligned 0 times 963s 5 (4.10%) aligned exactly 1 time 963s 9 (7.38%) aligned >1 times 963s 11.48% overall alignment rate 963s Read 50 alignments... 963s Read 100 alignments... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s TCGC 963s TCGC 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s CG 963s CG 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s AAGGG 963s AAGGG 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s AT 963s AT 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s GCA 963s GCA 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s GT 963s GT 963s Processing line... 963s TG 963s TG 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s ATAGTG 963s ATAGTG 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s CGAC 963s CGAC 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s CTC 963s CTC 963s Processing line... 963s Processing line... 963s CGACCGCG 963s CGACCGCG 963s /usr/bin/bowtie2 --score-min L,6.74256623867812,6.60348650407808 --trim5 7 -R 2 -D 16 --np 4 --nofw --ma 38.5561041977577 --large-index --rdg 11.3990264567161 --mp 8.11730078559861,2.32332866801086 --trim3 2 --cp-ival 1 --cp-min 3 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 963s Processing line... 963s TG 963s TG 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s GC 963s GC 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s CC 963s CC 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s --- Summary --- 963s Read 1 reference strings 963s Checked 14 alignments, 0 edits 963s --------------- 963s PASSED 963s ALSO checking that bowtie2 and bowtie2-align match up 963s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 963s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 963s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '2' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 963s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '11' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 963s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '16' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 963s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 963s Warning: skipping read '18' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 963s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '22' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 963s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '27' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 963s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '30' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 963s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '31' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 963s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '34' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 963s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '35' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 963s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '37' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 963s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '43' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 963s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '47' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 963s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '52' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 963s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '55' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 963s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '66' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 963s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '67' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 963s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '70' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 963s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '71' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 963s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '72' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 963s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '84' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 963s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '91' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 963s Warning: skipping read '97' because length (1) <= # seed mismatches (0) 963s Warning: skipping read '97' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 963s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '101' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 963s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '104' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 963s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '106' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 963s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '108' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 963s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '121' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 963s 122 reads; of these: 963s 122 (100.00%) were unpaired; of these: 963s 108 (88.52diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 963s /usr/bin/bowtie2 --score-min L,6.74256623867812,6.60348650407808 --trim5 7 -R 2 -D 16 --np 4 --nofw --ma 38.5561041977577 --large-index --rdg 11.3990264567161 --mp 8.11730078559861,2.32332866801086 --trim3 2 --cp-ival 1 --cp-min 3 -q -p 3 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 963s %) aligned 0 times 963s 5 (4.10%) aligned exactly 1 time 963s 9 (7.38%) aligned >1 times 963s 11.48% overall alignment rate 963s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 963s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 963s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 963s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '2' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 963s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '11' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 963s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '16' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 963s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 963s Warning: skipping read '18' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 963s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '22' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 963s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '27' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 963s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 963s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 963s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '34' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 963s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '35' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 963s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '37' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 963s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '43' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 963s Warning: skipping read '30' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 963s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '31' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 963s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '52' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 963s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '55' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 963s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '66' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 963s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '67' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 963s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '70' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 963s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '71' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 963s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '72' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 963s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '47' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 963s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '121' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 963s Warning: skipping read '97' because length (1) <= # seed mismatches (0) 963s Warning: skipping read '97' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 963s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '101' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 963s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '104' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 963s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '106' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 963s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '108' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 963s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '84' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 963s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '91' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 963s 122 reads; of these: 963s 122sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 963s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 963s (100.00%) were unpaired; of these: 963s 108 (88.52%) aligned 0 times 963s 5 (4.10%) aligned exactly 1 time 963s 9 (7.38%) aligned >1 times 963s 11.48% overall alignment rate 963s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 963s Flattened IUPAC characters 963s Mutating sequence Sim.pm.2 963s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 963s Finished SNPs 963s Finished ref gaps 963s Finished read gaps 963s Mutating sequence Sim.pm.1 963s Introducing 5 SNPs, 1/0 ref/read gaps, and 1 rearrangements 963s Finished SNPs 963s Finished ref gaps 963s Finished read gaps 963s Mutated reference genome to subject genome 963s SNPs introduced: 9 963s Reference gaps introduced: 2 963s Read gaps introduced: 0 963s Rearrangements introduced: 1 963s Created read sampler 963s Sampling 64 reads 963s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 963s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 963s parsing sequence Sim.pm.1... 963s parsing sequence Sim.pm.2... 963s Parsed 110 reference bases 963s *** Run 40 of 100 963s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --norc --nofw --large-index --score-min L,2.50402940662694,6.30805362071123 --trim5 7 --mp 7.7831000939773,5.02373098722526 -i C,0.13004360303921 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 963s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 963s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '1' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 963s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '4' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 963s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '10' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 963s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '11' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 963s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '13' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 963s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '17' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 963s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '18' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 963s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '19' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 963s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '23' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 963s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '24' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 963s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '28' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 963s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 963s Warning: skipping read '30' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 963s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '35' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 963s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '37' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 963s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '38' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 963s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '41' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 963s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '56' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 963s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '57' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 963s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 963s Warning: skipping read '58' because it was < 2 characters long 963s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 963s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 963s 64 reads; of these: 963s 64 (100.00%) were unpaired; of these: 963s 64 (100.00%) aligned 0 times 963s 0 (0.00%) aligned exactly 1 time 963s 0 (0.00%) aligned >1 times 963s 0.00% overall alignment rate 963s Read 50 alignments... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 963s Processing line... 964s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --norc --nofw --large-index --score-min L,2.50402940662694,6.30805362071123 --trim5 7 --mp 7.7831000939773,5.02373098722526 -i C,0.13004360303921 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s --- Summary --- 964s Read 1 reference strings 964s Checked 0 alignments, 0 edits 964s --------------- 964s PASSED 964s ALSO checking that bowtie2 and bowtie2-align match up 964s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 964s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '1' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 964s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '4' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 964s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '10' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 964s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '11' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 964s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '13' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 964s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '17' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 964s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '18' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 964s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '19' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 964s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '23' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 964s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '24' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 964s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '28' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 964s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 964s Warning: skipping read '30' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 964s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '35' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 964s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '37' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 964s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '38' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 964s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '41' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 964s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '56' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 964s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '57' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 964s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '58' because it was < 2 characters long 964s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 964s 64 reads; of these: 964s 64 (100.00%) were unpaired; of these: 964s 64 (100.00%) aligned 0 times 964s 0 (0.00%) aligned exactly 1 time 964s 0 (0.00%) aligned >1 times 964s 0.00% overall alignment rate 964s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 964s Flattened IUPAC characters 964s Mutating sequence Sim.pm.2 964s Introducing 11 SNPs, 0/0 ref/read gaps, and 1 rearrangements 964s Finished SNPs 964s Finished ref gaps 964s Finished read gaps 964s Mutating sequence Sim.pm.1 964s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 964s Finished SNPs 964s Finished ref gaps 964s Finished read gaps 964s Mutated reference genome to subject genome 964s SNPs introduced: 19 964s Reference gaps introduced: 0 964s Read gaps introduced: 1 964s Rearrangements introduced: 1 964s Created read sampler 964s Sampling 24 reads 964s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 964s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 964s parsing sequence Sim.pm.1... 964s parsing sequence Sim.pm.2... 964s Parsed 110 reference bases 964s *** Run 41 of 100 964s /usr/bin/bowtie2 --large-index -k 2 --trim3 4 --local --cp-ival 1 --mm --cp-min 3 --score-min L,6.12837793860218,5.50084691800735 --trim5 7 --rfg 45.688388341811,3.51189823425903 -i L,0.208462352500903 --nofw -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 964s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '1' because it was < 2 characters long 964s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '3' because it was < 2 characters long 964s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '6' because it was < 2 characters long 964s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '7' because it was < 2 characters long 964s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '12' because it was < 2 characters long 964s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 964s Warning: skipping read '18' because it was < 2 characters long 964s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '21' because it was < 2 characters long 964s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '22' because it was < 2 characters long 964s 24 reads; of these: 964s 24 (100.00%) were unpaired; of these: 964s 24 (100.00%) aligned 0 times 964s 0 (0.00%) aligned exactly 1 time 964s 0 (0.00%) aligned >1 times 964s 0.00% overall alignment rate 964s Processing line... 964s /usr/bin/bowtie2 --large-index -k 2 --trim3 4 --local --cp-ival 1 --mm --cp-min 3 --score-min L,6.12837793860218,5.50084691800735 --trim5 7 --rfg 45.688388341811,3.51189823425903 -i L,0.208462352500903 --nofw -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s --- Summary --- 964s Read 1 reference strings 964s Checked 0 alignments, 0 edits 964s --------------- 964s PASSED 964s ALSO checking that bowtie2 and bowtie2-align match up 964s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '1' because it was < 2 characters long 964s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '3' because it was < 2 characters long 964s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '6' because it was < 2 characters long 964s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '7' because it was < 2 characters long 964s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '12' because it was < 2 characters long 964s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 964s Warning: skipping read '18' because it was < 2 characters long 964s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '21' because it was < 2 characters long 964s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 964s Warning: skipping read '22' because it was < 2 characters long 964s 24 reads; of these: 964s 24 (100.00%) were unpaired; of these: 964s 24 (100.00%) aligned 0 times 964s 0 (0.00%) aligned exactly 1 time 964s 0 (0.00%) aligned >1 times 964s 0.00% overall alignment rate 964s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 964s Flattened IUPAC characters 964s Mutating sequence Sim.pm.2 964s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 964s Finished SNPs 964s Finished ref gaps 964s Finished read gaps 964s Mutating sequence Sim.pm.1 964s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 964s Finished SNPs 964s Finished ref gaps 964s Finished read gaps 964s Mutated reference genome to subject genome 964s SNPs introduced: 4 964s Reference gaps introduced: 0 964s Read gaps introduced: 0 964s Rearrangements introduced: 1 964s Created read sampler 964s Sampling 52 reads 964s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 964s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 964s parsing sequence Sim.pm.1... 964s parsing sequence Sim.pm.2... 964s Parsed 110 reference bases 964s *** Run 42 of 100 964s /usr/bin/bowtie2 --np 7 -R 3 --rfg 42.9288359884876,18.1459252696501 --score-min L,8.90889499860633,7.07270537418311 --cp-min 2 --cp-ival 3 --mm -a --mp 6.37685455616221,6.11464108002581 --trim3 0 --ma 23.6008743164476 --large-index -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 964s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 964s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 964s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 964s 52 reads; of these: 964s 52 (100.00%) were unpaired; of these: 964s 40 (76.92%) aligned 0 times 964s 8 (15.38%) aligned exactly 1 time 964s 4 (7.69%) aligned >1 times 964s 23.08% overall alignment rate 964s Read 50 alignments... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s GCATAGTGCGAC 964s GCATAGTGCGAC 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s TGC 964s TGC 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s TGC 964s TGC 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s AATGCAGATGGGACAGGGGAGGCGAACAAAGGGCCTCGCAGCG 964s AATGCAGATGGGACAGGGGAGGCGAACAAAGGGCCTCGCAGCG 964s Processing line... 964s Processing line... 964s GCATGTCCAGGGACGCACAGCATAGTGCGACCGCG 964s GCATGTCCAGGGACGCACAGCATAGTGCGACCGCG 964s /usr/bin/bowtie2 --np 7 -R 3 --rfg 42.9288359884876,18.1459252696501 --score-min L,8.90889499860633,7.07270537418311 --cp-min 2 --cp-ival 3 --mm -a --mp 6.37685455616221,6.11464108002581 --trim3 0 --ma 23.6008743164476 --large-index -r -p 3 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 964s Processing line... 964s Processing line... 964s ACAGGGGA 964s ACAGGGGA 964s Processing line... 964s CAG 964s CAG 964s Processing line... 964s CAG 964s CAG 964s Processing line... 964s CAG 964s CAG 964s Processing line... 964s CAG 964s CAG 964s Processing line... 964s CAG 964s CAG 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s GGGAG 964s GGGAG 964s Processing line... 964s Processing line... 964s Processing line... 964s ACAGGGG 964s ACAGGGG 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s TGC 964s TGC 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s TGC 964s TGC 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s Processing line... 964s GACGCACAGCATAGTG 964s GACGCACAGCATAGTG 964s Processing line... 964s Processing line... 964s Processing line... 964s GTCCAGGG 964s GTCCAGGG 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s TGC 964s TGC 964s Processing line... 964s TGC 964s TGC 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s GCA 964s GCA 964s Processing line... 964s Processing line... 964s --- Summary --- 964s Read 1 reference strings 964s Checked 34 alignments, 0 edits 964s --------------- 964s PASSED 964s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 965s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 965s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 965s 52 reads; of these: 965s 52 (100.00%) were unpaired; of these: 965s 40 (76.92%) aligned 0 times 965s 8 (15.38%) aligned exactly 1 time 965s 4 (7.69%) aligned >1 times 965s 23.08% overall alignment rate 965s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 965s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 965s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 965s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 965s /usr/bin/bowtie2 --np 7 -R 3 --rfg 42.9288359884876,18.1459252696501 --score-min L,8.90889499860633,7.07270537418311 --cp-min 2 --cp-ival 3 --mm -a --mp 6.37685455616221,6.11464108002581 --trim3 0 --ma 23.6008743164476 --large-index -r -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 965s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 965s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 965s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 965s 52 reads; of these: 965s 52 (100.00%) were unpaired; of these: 965s 40 (76.92%) aligned 0 times 965s 8 (15.38%) aligned exactly 1 time 965s 4 (7.69%) aligned >1 times 965s 23.08% overall alignment rate 965s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 965s Flattened IUPAC characters 965s Mutating sequence Sim.pm.1 965s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 965s Finished SNPs 965s Finished ref gaps 965s Finished read gaps 965s Mutating sequence Sim.pm.2 965s Introducing 12 SNPs, 2/0 ref/read gaps, and 0 rearrangements 965s Finished SNPs 965s Finished ref gaps 965s Finished read gaps 965s Mutated reference genome to subject genome 965s SNPs introduced: 22 965s Reference gaps introduced: 2 965s Read gaps introduced: 0 965s Rearrangements introduced: 1 965s Created read sampler 965s Sampling 105 reads 965s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 965s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 965s parsing sequence Sim.pm.1... 965s *** Run 43 of 100 965s /usr/bin/bowtie2 --large-index --local --trim3 5 -a --rdg 44.4441223543838 --cp-ival 1 --mm --cp-min 3 --score-min L,8.73993801087827,9.05812317316442 -R 3 -D 38 -N 1 -L18 --nofw --np 1 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 965s parsing sequence Sim.pm.2... 965s Parsed 110 reference bases 965s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '6' because it was < 2 characters long 965s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '8' because it was < 2 characters long 965s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '19' because it was < 2 characters long 965s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '27' because it was < 2 characters long 965s Warning: skipping read '29' because length (1) <= # seed mismatches (1) 965s Warning: skipping read '29' because it was < 2 characters long 965s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '30' because it was < 2 characters long 965s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '47' because it was < 2 characters long 965s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '48' because it was < 2 characters long 965s Warning: skipping read '59' because length (1) <= # seed mismatches (1) 965s Warning: skipping read '59' because it was < 2 characters long 965s Warning: skipping read '66' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '66' because it was < 2 characters long 965s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '70' because it was < 2 characters long 965s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '80' because it was < 2 characters long 965s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '81' because it was < 2 characters long 965s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '83' because it was < 2 characters long 965s Warning: skipping read '84' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '84' because it was < 2 characters long 965s Warning: skipping read '93' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '93' because it was < 2 characters long 965s Warning: skipping read '95' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '95' because it was < 2 characters long 965s 105 reads; of these: 965s 105 (100.00%) were unpaired; of these: 965s 105 (100.00%) aligned 0 times 965s 0 (0.00%) aligned exactly 1 time 965s 0 (0.00%) aligned >1 times 965s 0.00% overall alignment rate 965s Read 50 alignments... 965s Read 100 alignments... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s /usr/bin/bowtie2 --large-index --local --trim3 5 -a --rdg 44.4441223543838 --cp-ival 1 --mm --cp-min 3 --score-min L,8.73993801087827,9.05812317316442 -R 3 -D 38 -N 1 -L18 --nofw --np 1 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s Processing line... 965s --- Summary --- 965s Read 1 reference strings 965s Checked 0 alignments, 0 edits 965s --------------- 965s PASSED 965s ALSO checking that bowtie2 and bowtie2-align match up 965s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '6' because it was < 2 characters long 965s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '8' because it was < 2 characters long 965s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '19' because it was < 2 characters long 965s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '27' because it was < 2 characters long 965s Warning: skipping read '29' because length (1) <= # seed mismatches (1) 965s Warning: skipping read '29' because it was < 2 characters long 965s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '30' because it was < 2 characters long 965s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '47' because it was < 2 characters long 965s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '48' because it was < 2 characters long 965s Warning: skipping read '59' because length (1) <= # seed mismatches (1) 965s Warning: skipping read '59' because it was < 2 characters long 965s Warning: skipping read '66' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '66' because it was < 2 characters long 965s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '70' because it was < 2 characters long 965s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '80' because it was < 2 characters long 965s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '81' because it was < 2 characters long 965s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '83' because it was < 2 characters long 965s Warning: skipping read '84' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '84' because it was < 2 characters long 965s Warning: skipping read '93' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '93' because it was < 2 characters long 965s Warning: skipping read '95' because length (0) <= # seed mismatches (1) 965s Warning: skipping read '95' because it was < 2 characters long 965s 105 reads; of these: 965s 105 (100.00%) were unpaired; of these: 965s 105 (100.00%) aligned 0 times 965s 0 (0.00%) aligned exactly 1 time 965s 0 (0.00%) aligned >1 times 965s 0.00% overall alignment rate 965s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 965s Flattened IUPAC characters 965s Mutating sequence Sim.pm.1 965s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 965s Finished SNPs 965s Finished ref gaps 965s Finished read gaps 965s Mutating sequence Sim.pm.2 965s Introducing 7 SNPs, 0/0 ref/read gaps, and 2 rearrangements 965s Finished SNPs 965s Finished ref gaps 965s Finished read gaps 965s Mutated reference genome to subject genome 965s SNPs introduced: 11 965s Reference gaps introduced: 1 965s Read gaps introduced: 0 965s Rearrangements introduced: 2 965s Created read sampler 965s Sampling 89 reads 965s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 965s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 965s parsing sequence Sim.pm.1... 965s parsing sequence Sim.pm.2... 965s Parsed 110 reference bases 965s *** Run 44 of 100 965s /usr/bin/bowtie2 -N 0 -L17 --cp-ival 3 --cp-min 2 --nofw --large-index --score-min L,7.19181617084163,5.90315026127164 -k 5 --rdg 4.89518027663712,10.4076191650925 --mp 8.31712241468737,1.4985024078622 --local -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 966s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #2 of read '55' because it was < 2 characters long 966s Read 50 alignments... 966s Read 100 alignments... 966s Warning: skipping mate #1 of read '87' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '87' because it was < 2 characters long 966s 89 reads; of these: 966s 89 (100.00%) were paired; of these: 966s 89 (100.00%) aligned concordantly 0 times 966s 0 (0.00%) aligned concordantly exactly 1 time 966s 0 (0.00%) aligned concordantly >1 times 966s ---- 966s 89 pairs aligned concordantly 0 times; of these: 966s 0 (0.00%) aligned discordantly 1 time 966s ---- 966s 89 pairs aligned 0 times concordantly or discordantly; of these: 966s 178 mates make up the pairs; of these: 966s 178 (100.00%) aligned 0 times 966s 0 (0.00%) aligned exactly 1 time 966s 0 (0.00%) aligned >1 times 966s 0.00% overall alignment rate 966s Read 150 alignments... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s --- Summary --- 966s Read 1 reference strings 966s Checked 0 alignments, 0 edits 966s --------------- 966s PASSED 966s Flattened IUPAC characters 966s Mutating sequence Sim.pm.2 966s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 966s Finished SNPs 966s Finished ref gaps 966s Finished read gaps 966s Mutating sequence Sim.pm.1 966s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 966s Finished SNPs 966s Finished ref gaps 966s Finished read gaps 966s Mutated reference genome to subject genome 966s SNPs introduced: 7 966s Reference gaps introduced: 0 966s Read gaps introduced: 0 966s Rearrangements introduced: 1 966s Created read sampler 966s Sampling 220 reads 966s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 966s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 966s parsing sequence Sim.pm.1... 966s parsing sequence Sim.pm.2... 966s Parsed 110 reference bases 966s *** Run 45 of 100 966s /usr/bin/bowtie2 -a --trim3 6 --local --large-index --cp-min 7 --cp-ival 1 --trim5 9 --score-min L,9.24980188777352,9.77800894441584 --norc --np 2 -D 37 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 966s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '2' because it was < 2 characters long 966s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '6' because it was < 2 characters long 966s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '11' because it was < 2 characters long 966s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '13' because it was < 2 characters long 966s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '14' because it was < 2 characters long 966s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '20' because it was < 2 characters long 966s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '23' because it was < 2 characters long 966s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '24' because it was < 2 characters long 966s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '27' because it was < 2 characters long 966s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '30' because it was < 2 characters long 966s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '34' because it was < 2 characters long 966s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '35' because it was < 2 characters long 966s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '36' because it was < 2 characters long 966s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '37' because it was < 2 characters long 966s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '46' because it was < 2 characters long 966s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '48' because it was < 2 characters long 966s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '49' because it was < 2 characters long 966s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '59' because it was < 2 characters long 966s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '69' because it was < 2 characters long 966s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '70' because it was < 2 characters long 966s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '71' because it was < 2 characters long 966s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '74' because it was < 2 characters long 966s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '77' because it was < 2 characters long 966s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '79' because it was < 2 characters long 966s Read 50 alignments... 966s Read 100 alignments... 966s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '84' because it was < 2 characters long 966s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '86' because it was < 2 characters long 966s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '87' because it was < 2 characters long 966s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '91' because it was < 2 characters long 966s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '92' because it was < 2 characters long 966s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '93' because it was < 2 characters long 966s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '100' because it was < 2 characters long 966s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '101' because it was < 2 characters long 966s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '108' because it was < 2 characters long 966s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '113' because it was < 2 characters long 966s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '116' because it was < 2 characters long 966s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '119' because it was < 2 characters long 966s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '120' because it was < 2 characters long 966s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '122' because it was < 2 characters long 966s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '123' because it was < 2 characters long 966s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '128' because it was < 2 characters long 966s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '130' because it was < 2 characters long 966s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '133' because it was < 2 characters long 966s Warning: skipping mate #2 of read '135' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #2 of read '135' because it was < 2 characters long 966s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '136' because it was < 2 characters long 966s Read 150 alignments... 966s Read 200 alignments... 966s Warning: skipping read '151' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '151' because it was < 2 characters long 966s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '153' because it was < 2 characters long 966s Warning: skipping read '155' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '155' because it was < 2 characters long 966s Warning: skipping mate #1 of read '157' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '157' because it was < 2 characters long 966s Warning: skipping mate #1 of read '160' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '160' because it was < 2 characters long 966s Warning: skipping mate #1 of read '161' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '161' because it was < 2 characters long 966s Warning: skipping mate #1 of read '162' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '162' because it was < 2 characters long 966s Warning: skipping mate #1 of read '166' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '166' because it was < 2 characters long 966s Warning: skipping mate #1 of read '167' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #2 of read '167' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '167' because it was < 2 characters long 966s Warning: skipping mate #2 of read '167' because it was < 2 characters long 966s Warning: skipping mate #1 of read '169' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '169' because it was < 2 characters long 966s Warning: skipping mate #1 of read '170' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '170' because it was < 2 characters long 966s Warning: skipping mate #1 of read '171' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '171' because it was < 2 characters long 966s Warning: skipping read '173' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '173' because it was < 2 characters long 966s Warning: skipping mate #1 of read '177' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '177' because it was < 2 characters long 966s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '180' because it was < 2 characters long 966s Warning: skipping mate #1 of read '183' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '183' because it was < 2 characters long 966s Warning: skipping read '194' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '194' because it was < 2 characters long 966s Warning: skipping read '195' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '195' because it was < 2 characters long 966s Warning: skipping mate #1 of read '196' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '196' because it was < 2 characters long 966s Warning: skipping read '198' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '198' because it was < 2 characters long 966s Warning: skipping read '199' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '199' because it was < 2 characters long 966s Warning: skipping read '202' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '202' because it was < 2 characters long 966s Warning: skipping read '208' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '208' because it was < 2 characters long 966s Read 250 alignments... 966s Read 300 alignments... 966s Warning: skipping mate #1 of read '210' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '210' because it was < 2 characters long 966s Warning: skipping mate #1 of read '211' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '211' because it was < 2 characters long 966s Warning: skipping mate #1 of read '215' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '215' because it was < 2 characters long 966s Warning: skipping mate #1 of read '219' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '219' because it was < 2 characters long 966s 220 reads; of these: 966s 165 (75.00%) were paired; of these: 966s 165 (100.00%) aligned concordantly 0 times 966s 0 (0.00%) aligned concordantly exactly 1 time 966s 0 (0.00%) aligned concordantly >1 times 966s ---- 966s 165 pairs aligned concordantly 0 times; of these: 966s 0 (0.00%) aligned discordantly 1 time 966s ---- 966s 165 pairs aligned 0 times concordantly or discordantly; of these: 966s 330 mates make up the pairs; of these: 966s 330 (100.00%) aligned 0 times 966s 0 (0.00%) aligned exactly 1 time 966s 0 (0.00%) aligned >1 times 966s 55 (25.00%) were unpaired; of these: 966s 55 (100.00%) aligned 0 times 966s 0 (0.00%) aligned exactly 1 time 966s 0 (0.00%) aligned >1 times 966s 0.00% overall alignment rate 966s Read 350 alignments... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s /usr/bin/bowtie2 -a --trim3 6 --local --large-index --cp-min 7 --cp-ival 1 --trim5 9 --score-min L,9.24980188777352,9.77800894441584 --norc --np 2 -D 37 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s Processing line... 966s --- Summary --- 966s Read 1 reference strings 966s Checked 0 alignments, 0 edits 966s --------------- 966s PASSED 966s ALSO checking that bowtie2 and bowtie2-align match up 966s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '2' because it was < 2 characters long 966s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '6' because it was < 2 characters long 966s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '11' because it was < 2 characters long 966s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '13' because it was < 2 characters long 966s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '14' because it was < 2 characters long 966s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '20' because it was < 2 characters long 966s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '23' because it was < 2 characters long 966s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '24' because it was < 2 characters long 966s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '27' because it was < 2 characters long 966s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '30' because it was < 2 characters long 966s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '34' because it was < 2 characters long 966s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '35' because it was < 2 characters long 966s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '36' because it was < 2 characters long 966s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '37' because it was < 2 characters long 966s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '46' because it was < 2 characters long 966s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '48' because it was < 2 characters long 966s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '49' because it was < 2 characters long 966s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '59' because it was < 2 characters long 966s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '69' because it was < 2 characters long 966s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '70' because it was < 2 characters long 966s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '71' because it was < 2 characters long 966s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '74' because it was < 2 characters long 966s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '77' because it was < 2 characters long 966s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '79' because it was < 2 characters long 966s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '84' because it was < 2 characters long 966s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '86' because it was < 2 characters long 966s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '87' because it was < 2 characters long 966s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '91' because it was < 2 characters long 966s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '92' because it was < 2 characters long 966s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '93' because it was < 2 characters long 966s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '100' because it was < 2 characters long 966s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '101' because it was < 2 characters long 966s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '108' because it was < 2 characters long 966s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '113' because it was < 2 characters long 966s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '116' because it was < 2 characters long 966s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '119' because it was < 2 characters long 966s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '120' because it was < 2 characters long 966s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '122' because it was < 2 characters long 966s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '123' because it was < 2 characters long 966s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '128' because it was < 2 characters long 966s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '130' because it was < 2 characters long 966s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '133' because it was < 2 characters long 966s Warning: skipping mate #2 of read '135' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #2 of read '135' because it was < 2 characters long 966s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '136' because it was < 2 characters long 966s Warning: skipping read '151' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '151' because it was < 2 characters long 966s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '153' because it was < 2 characters long 966s Warning: skipping read '155' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '155' because it was < 2 characters long 966s Warning: skipping mate #1 of read '157' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '157' because it was < 2 characters long 966s Warning: skipping mate #1 of read '160' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '160' because it was < 2 characters long 966s Warning: skipping mate #1 of read '161' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '161' because it was < 2 characters long 966s Warning: skipping mate #1 of read '162' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '162' because it was < 2 characters long 966s Warning: skipping mate #1 of read '166' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '166' because it was < 2 characters long 966s Warning: skipping mate #1 of read '167' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #2 of read '167' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '167' because it was < 2 characters long 966s Warning: skipping mate #2 of read '167' because it was < 2 characters long 966s Warning: skipping mate #1 of read '169' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '169' because it was < 2 characters long 966s Warning: skipping mate #1 of read '170' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '170' because it was < 2 characters long 966s Warning: skipping mate #1 of read '171' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '171' because it was < 2 characters long 966s Warning: skipping read '173' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '173' because it was < 2 characters long 966s Warning: skipping mate #1 of read '177' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '177' because it was < 2 characters long 966s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '180' because it was < 2 characters long 966s Warning: skipping mate #1 of read '183' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '183' because it was < 2 characters long 966s Warning: skipping read '194' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '194' because it was < 2 characters long 966s Warning: skipping read '195' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '195' because it was < 2 characters long 966s Warning: skipping mate #1 of read '196' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '196' because it was < 2 characters long 966s Warning: skipping read '198' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '198' because it was < 2 characters long 966s Warning: skipping read '199' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '199' because it was < 2 characters long 966s Warning: skipping read '202' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '202' because it was < 2 characters long 966s Warning: skipping read '208' because length (0) <= # seed mismatches (0) 966s Warning: skipping read '208' because it was < 2 characters long 966s Warning: skipping mate #1 of read '210' because length (1) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '210' because it was < 2 characters long 966s Warning: skipping mate #1 of read '211' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '211' because it was < 2 characters long 966s Warning: skipping mate #1 of read '215' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '215' because it was < 2 characters long 966s Warning: skipping mate #1 of read '219' because length (0) <= # seed mismatches (0) 966s Warning: skipping mate #1 of read '219' because it was < 2 characters long 966s 220 reads; of these: 966s 165 (75.00%) were paired; of these: 966s 165 (100.00%) aligned concordantly 0 times 966s 0 (0.00%) aligned concordantly exactly 1 time 966s 0 (0.00%) aligned concordantly >1 times 966s ---- 966s 165 pairs aligned concordantly 0 times; of these: 966s 0 (0.00%) aligned discordantly 1 time 966s ---- 966s 165 pairs aligned 0 times concordantly or discordantly; of these: 966s 330 mates make up the pairs; of these: 966s 330 (100.00%) aligned 0 times 966s 0 (0.00%) aligned exactly 1 time 966s 0 (0.00%) aligned >1 times 966s 55 (25.00%) were unpaired; of these: 966s 55 (100.00%) aligned 0 times 966s 0 (0.00%) aligned exactly 1 time 966s 0 (0.00%) aligned >1 times 966s 0.00% overall alignment rate 966s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 966s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 966s /usr/bin/bowtie2 -a --trim3 6 --local --large-index --cp-min 7 --cp-ival 1 --trim5 9 --score-min L,9.24980188777352,9.77800894441584 --norc --np 2 -D 37 -f -p 3 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 967s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '2' because it was < 2 characters long 967s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '6' because it was < 2 characters long 967s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '11' because it was < 2 characters long 967s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '13' because it was < 2 characters long 967s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '14' because it was < 2 characters long 967s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '20' because it was < 2 characters long 967s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '23' because it was < 2 characters long 967s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '24' because it was < 2 characters long 967s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '27' because it was < 2 characters long 967s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '30' because it was < 2 characters long 967s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '34' because it was < 2 characters long 967s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '35' because it was < 2 characters long 967s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '36' because it was < 2 characters long 967s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '37' because it was < 2 characters long 967s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '49' because it was < 2 characters long 967s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '46' because it was < 2 characters long 967s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '48' because it was < 2 characters long 967s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '69' because it was < 2 characters long 967s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '70' because it was < 2 characters long 967s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '71' because it was < 2 characters long 967s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '74' because it was < 2 characters long 967s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '77' because it was < 2 characters long 967s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '79' because it was < 2 characters long 967s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '59' because it was < 2 characters long 967s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '84' because it was < 2 characters long 967s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '86' because it was < 2 characters long 967s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '87' because it was < 2 characters long 967s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '91' because it was < 2 characters long 967s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '92' because it was < 2 characters long 967s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '93' because it was < 2 characters long 967s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '113' because it was < 2 characters long 967s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '116' because it was < 2 characters long 967s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '100' because it was < 2 characters long 967s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '101' because it was < 2 characters long 967s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '130' because it was < 2 characters long 967s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '133' because it was < 2 characters long 967s Warning: skipping mate #2 of read '135' because length (1) <= # seed mismatches (0) 967s Warning: skipping mate #2 of read '135' because it was < 2 characters long 967s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '136' because it was < 2 characters long 967s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '108' because it was < 2 characters long 967s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '119' because it was < 2 characters long 967s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '120' because it was < 2 characters long 967s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '122' because it was < 2 characters long 967s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '123' because it was < 2 characters long 967s Warning: skipping mate #1 of read '161' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '161' because it was < 2 characters long 967s Warning: skipping mate #1 of read '162' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '162' because it was < 2 characters long 967s Warning: skipping mate #1 of read '166' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '166' because it was < 2 characters long 967s Warning: skipping mate #1 of read '167' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #2 of read '167' because length (1) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '167' because it was < 2 characters long 967s Warning: skipping mate #2 of read '167' because it was < 2 characters long 967s Warning: skipping mate #1 of read '169' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '169' because it was < 2 characters long 967s Warning: skipping mate #1 of read '170' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '170' because it was < 2 characters long 967s Warning: skipping read '151' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '151' because it was < 2 characters long 967s Warning: skipping mate #1 of read '171' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '171' because it was < 2 characters long 967s Warning: skipping read '173' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '173' because it was < 2 characters long 967s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '153' because it was < 2 characters long 967s Warning: skipping read '155' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '155' because it was < 2 characters long 967s Warning: skipping mate #1 of read '157' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '157' because it was < 2 characters long 967s Warning: skipping mate #1 of read '160' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '160' because it was < 2 characters long 967s Warning: skipping mate #1 of read '177' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '177' because it was < 2 characters long 967s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '128' because it was < 2 characters long 967s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '194' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '194' because it was < 2 characters long 967s Warning: skipping read '195' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '195' because it was < 2 characters long 967s Warning: skipping mate #1 of read '196' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '196' because it was < 2 characters long 967s Warning: skipping read '198' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '198' because it was < 2 characters long 967s Warning: skipping read '199' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '199' because it was < 2 characters long 967s Warning: skipping read '202' because length (0) <= # seed mismatches (0) 967s Warning: skipping read '202' because it was < 2 characters long 967s Warning: skipping mate #1 of read '180' because it was < 2 characters long 967s Warning: skipping mate #1 of read '183' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '183' because it was < 2 characters long 967s Warning: skipping mate #1 of read '210' because length (1) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '210' because it was < 2 characters long 967s Warning: skipping mate #1 of read '211' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '211' because it was < 2 characters long 967s Warning: skipping read '208' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '215' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '215' because it was < 2 characters long 967s Warning: skipping mate #1 of read '219' because length (0) <= # seed mismatches (0) 967s Warning: skipping mate #1 of read '219' because it was < 2 characters long 967s Warning: skipping read '208' because it was < 2 characters long 967s 220 reads; of these: 967s 165 (75.00%) were paired; of these: 967s 165 (100.00%) aligned concordantly 0 times 967s 0 (0.00%) aligned concordantly exactly 1 time 967s 0 (0.00%) aligned concordantly >1 times 967s ---- 967s 165 pairs aligned concordantly 0 times; of these: 967s 0 (0.00%) aligned discordantly 1 time 967s ---- 967s 165 pairs aligned 0 times concordantly or discordantly; of these: 967s 330 mates make up the pairs; of these: 967s 330 (100.00%) aligned 0 times 967s 0 (0.00%) aligned exactly 1 time 967s 0 (0.00%) aligned >1 times 967s 55 (25.00%) were unpaired; of these: 967s 55 (100.00%) aligned 0 times 967s 0 (0.00%) aligned exactly 1 time 967s 0 (0.00%) aligned >1 times 967s 0.00% overall alignment rate 967s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 967s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 967s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 967s Flattened IUPAC characters 967s Mutating sequence Sim.pm.1 967s Introducing 1 SNPs, 3/1 ref/read gaps, and 0 rearrangements 967s Finished SNPs 967s Finished ref gaps 967s Finished read gaps 967s Mutating sequence Sim.pm.2 967s Introducing 8 SNPs, 0/1 ref/read gaps, and 1 rearrangements 967s Finished SNPs 967s Finished ref gaps 967s Finished read gaps 967s Mutated reference genome to subject genome 967s SNPs introduced: 9 967s Reference gaps introduced: 3 967s Read gaps introduced: 2 967s Rearrangements introduced: 1 967s Created read sampler 967s Sampling 156 reads 967s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 967s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 967s parsing sequence Sim.pm.1... 967s parsing sequence Sim.pm.2... 967s Parsed 110 reference bases 967s *** Run 46 of 100 967s /usr/bin/bowtie2 --cp-min 4 --mm --cp-ival 2 --rdg 20.6763429676598 --mp 8.70891118387573,3.45523702292477 --large-index -M 5 --norc --nofw -R 4 --n-ceil 0.764367822078646,1.21107122927953 --score-min L,3.07073006593252,9.84198933400637 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 967s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 967s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 967s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '33' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 967s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '66' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 967s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '82' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 967s Warning: skipping read '103' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '103' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 967s Warning: skipping read '105' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '105' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 967s Warning: skipping read '108' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '108' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 967s Warning: skipping read '139' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '139' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 967s 156 reads; of these: 967s 156 (100.00%) were unpaired; of these: 967s 156 (100.00%) aligned 0 times 967s 0 (0.00%) aligned exactly 1 time 967s 0 (0.00%) aligned >1 times 967s 0.00% overall alignment rate 967s Read 50 alignments... 967s Read 100 alignments... 967s Read 150 alignments... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s /usr/bin/bowtie2 --cp-min 4 --mm --cp-ival 2 --rdg 20.6763429676598 --mp 8.70891118387573,3.45523702292477 --large-index -M 5 --norc --nofw -R 4 --n-ceil 0.764367822078646,1.21107122927953 --score-min L,3.07073006593252,9.84198933400637 -q -p 3 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s Processing line... 967s --- Summary --- 967s Read 1 reference strings 967s Checked 0 alignments, 0 edits 967s --------------- 967s PASSED 967s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 967s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 967s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 967s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '33' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 967s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '66' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 967s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '82' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 967s Warning: skipping read '103' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '103' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 967s Warning: skipping read '105' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '105' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 967s Warning: skipping read '108' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '108' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 967s Warning: skipping read '139' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '139' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 967s 156 reads; of these: 967s 156 (100.00%) were unpaired; of these: 967s 156 (100.00%) aligned 0 times 967s 0 (0.00%) aligned exactly 1 time 967s 0 (0.00%) aligned >1 times 967s 0.00% overall alignment rate 967s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 967s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 967s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 967s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 967s /usr/bin/bowtie2 --cp-min 4 --mm --cp-ival 2 --rdg 20.6763429676598 --mp 8.70891118387573,3.45523702292477 --large-index -M 5 --norc --nofw -R 4 --n-ceil 0.764367822078646,1.21107122927953 --score-min L,3.07073006593252,9.84198933400637 -q -p 4 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 967s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 967s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 967s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '33' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 967s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '66' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 967s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '82' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 967s Warning: skipping read '103' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '103' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 967s Warning: skipping read '105' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '105' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 967s Warning: skipping read '108' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '108' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 967s Warning: skipping read '139' because length (1) <= # seed mismatches (0) 967s Warning: skipping read '139' because it was < 2 characters long 967s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 967s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 967s 156 reads; of these: 967s 156 (100.00%) were unpaired; of these: 967s 156 (100.00%) aligned 0 times 967s 0 (0.00%) aligned exactly 1 time 967s 0 (0.00%) aligned >1 times 967s 0.00% overall alignment rate 967s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 967s Flattened IUPAC characters 967s Mutating sequence Sim.pm.1 967s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 967s Finished SNPs 967s Finished ref gaps 967s Finished read gaps 967s Mutating sequence Sim.pm.2 967s Introducing 1 SNPs, 0/0 ref/read gaps, and 2 rearrangements 967s Finished SNPs 967s Finished ref gaps 967s Finished read gaps 967s Mutated reference genome to subject genome 967s SNPs introduced: 9 967s Reference gaps introduced: 0 967s Read gaps introduced: 0 967s Rearrangements introduced: 3 967s Created read sampler 967s Sampling 52 reads 967s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 967s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 967s parsing sequence Sim.pm.1... 967s parsing sequence Sim.pm.2... 967s Parsed 110 reference bases 967s *** Run 47 of 100 967s /usr/bin/bowtie2 --trim5 7 --score-min L,2.2014104407839,7.41940562969515 --gbar 1 --norc --mp 4.90496252846057,4.69663270153747 --large-index --ma 21.1872856979814 --cp-min 3 --cp-ival 1 --mm -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 968s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 968s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 968s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '9' because it was < 2 characters long 968s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 968s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '11' because it was < 2 characters long 968s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 968s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '19' because it was < 2 characters long 968s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 968s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '29' because it was < 2 characters long 968s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 968s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '34' because it was < 2 characters long 968s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 968s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '36' because it was < 2 characters long 968s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 968s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '40' because it was < 2 characters long 968s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 968s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '41' because it was < 2 characters long 968s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 968s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 968s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '52' because it was < 2 characters long 968s 52 reads; of these: 968s 52 (100.00%) were unpaired; of these: 968s 43 (82.69%) aligned 0 times 968s 6 (11.54%) aligned exactly 1 time 968s 3 (5.77%) aligned >1 times 968s 17.31% overall alignment rate 968s Read 50 alignments... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s CAGC 968s CAGC 968s Processing line... 968s Processing line... 968s CAGC 968s CAGC 968s Processing line... 968s Processing line... 968s Processing line... 968s CAGATGGGACAGGGGAGGCGAACAA 968s CAGATGGGACAGGGGAGGCGAACAA 968s Processing line... 968s ATGG 968s ATGG 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s GGGACAGGGGAGGCGAACAAA 968s GGGACAGGGGAGGCGAACAAA 968s Processing line... 968s Processing line... 968s TC 968s TC 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s ATGCAGATGGG 968s ATGCAGATGGG 968s Processing line... 968s Processing line... 968s GGGACAGGGGAGGCGAACAAA 968s GGGACAGGGGAGGCGAACAAA 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s GACCGCG 968s GACCGCG 968s Processing line... 968s Processing line... 968s Processing line... 968s --- Summary --- 968s Read 1 reference strings 968s Checked 9 alignments, 0 edits 968s --------------- 968s PASSED 968s Flattened IUPAC characters 968s Mutating sequence Sim.pm.1 968s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 968s Finished SNPs 968s Finished ref gaps 968s Finished read gaps 968s Mutating sequence Sim.pm.2 968s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 968s Finished SNPs 968s Finished ref gaps 968s Finished read gaps 968s Mutated reference genome to subject genome 968s SNPs introduced: 7 968s Reference gaps introduced: 1 968s Read gaps introduced: 0 968s Rearrangements introduced: 1 968s Created read sampler 968s Sampling 121 reads 968s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 968s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 968s parsing sequence Sim.pm.1... 968s parsing sequence Sim.pm.2... 968s Parsed 110 reference bases 968s *** Run 48 of 100 968s /usr/bin/bowtie2 --local --rfg 29.7320891833993,6.40308040625501 --trim5 5 --score-min L,1.30983458195624,6.91961372465229 --large-index --cp-min 4 --cp-ival 1 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 968s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 968s Warning: skipping mate #2 of read '3' because it was < 2 characters long 968s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '11' because it was < 2 characters long 968s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '13' because it was < 2 characters long 968s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '20' because it was < 2 characters long 968s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '34' because it was < 2 characters long 968s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 968s Warning: skipping mate #2 of read '43' because it was < 2 characters long 968s Warning: skipping mate #1 of read '45' because length (1) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '45' because it was < 2 characters long 968s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '62' because it was < 2 characters long 968s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '64' because it was < 2 characters long 968s Read 50 alignments... 968s Read 100 alignments... 968s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '72' because it was < 2 characters long 968s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '78' because it was < 2 characters long 968s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '79' because it was < 2 characters long 968s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '85' because it was < 2 characters long 968s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '92' because it was < 2 characters long 968s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '94' because it was < 2 characters long 968s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '105' because it was < 2 characters long 968s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '109' because it was < 2 characters long 968s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '112' because it was < 2 characters long 968s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '118' because it was < 2 characters long 968s 121 reads; of these: 968s 105 (86.78%) were paired; of these: 968s 105 (100.00%) aligned concordantly 0 times 968s 0 (0.00%) aligned concordantly exactly 1 time 968s 0 (0.00%) aligned concordantly >1 times 968s ---- 968s 105 pairs aligned concordantly 0 times; of these: 968s 0 (0.00%) aligned discordantly 1 time 968s ---- 968s 105 pairs aligned 0 times concordantly or discordantly; of these: 968s 210 mates make up the pairs; of these: 968s 210 (100.00%) aligned 0 times 968s 0 (0.00%) aligned exactly 1 time 968s 0 (0.00%) aligned >1 times 968s 16 (13.22%) were unpaired; of these: 968s 16 (100.00%) aligned 0 times 968s 0 (0.00%) aligned exactly 1 time 968s 0 (0.00%) aligned >1 times 968s 0.00% overall alignment rate 968s Read 150 alignments... 968s Read 200 alignments... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s /usr/bin/bowtie2 --local --rfg 29.7320891833993,6.40308040625501 --trim5 5 --score-min L,1.30983458195624,6.91961372465229 --large-index --cp-min 4 --cp-ival 1 -f -p 3 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s Processing line... 968s --- Summary --- 968s Read 1 reference strings 968s Checked 0 alignments, 0 edits 968s --------------- 968s PASSED 968s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 968s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 968s Warning: skipping mate #2 of read '3' because it was < 2 characters long 968s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '11' because it was < 2 characters long 968s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '13' because it was < 2 characters long 968s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '34' because it was < 2 characters long 968s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 968s Warning: skipping mate #2 of read '43' because it was < 2 characters long 968s Warning: skipping mate #1 of read '45' because length (1) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '45' because it was < 2 characters long 968s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '20' because it was < 2 characters long 968s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 968s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '85' because it was < 2 characters long 968s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '92' because it was < 2 characters long 968s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '94' because it was < 2 characters long 968s Warning: skipping read '72' because it was < 2 characters long 968s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '78' because it was < 2 characters long 968s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '79' because it was < 2 characters long 968s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '118' because it was < 2 characters long 968s Warning: skipping mate #1 of read '62' because it was < 2 characters long 968s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '64' because it was < 2 characters long 968s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '105' because it was < 2 characters long 968s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 968s Warning: skipping read '109' because it was < 2 characters long 968s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 968s Warning: skipping mate #1 of read '112' because it was < 2 characters long 968s 121 reads; of these: 968s 105 (86.78%) were paired; of these: 968s 105 (100.00%) aligned concordantly 0 times 968s 0 (0.00%) aligned concordantly exactly 1 time 968s 0 (0.00%) aligned concordantly >1 times 968s ---- 968s 105 pairs aligned concordantly 0 times; of these: 968s 0 (0.00%) aligned discordantly 1 time 968s ---- 968s 105 pairs aligned 0 times concordantly or discordantly; of these: 968s 210 mates make up the pairs; of these: 968s 210 (100.00%) aligned 0 times 968s 0 (0.00%) aligned exactly 1 time 968s 0 (0.00%) aligned >1 times 968s 16 (13.22%) were unpaired; of these: 968s 16 (100.00%) aligned 0 times 968s 0 (0.00%) aligned exactly 1 time 968s 0 (0.00%) aligned >1 times 968s 0.00% overall alignment rate 968s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 968s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 968s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 968s Flattened IUPAC characters 968s Mutating sequence Sim.pm.1 968s Introducing 7 SNPs, 0/1 ref/read gaps, and 1 rearrangements 968s Finished SNPs 968s Finished ref gaps 968s Finished read gaps 968s Mutating sequence Sim.pm.2 968s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 968s Finished SNPs 968s Finished ref gaps 968s Finished read gaps 968s Mutated reference genome to subject genome 968s SNPs introduced: 10 968s Reference gaps introduced: 0 968s Read gaps introduced: 1 968s Rearrangements introduced: 2 968s Created read sampler 968s Sampling 108 reads 968s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 968s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 968s parsing sequence Sim.pm.1... 968s parsing sequence Sim.pm.2... 968s Parsed 110 reference bases 968s *** Run 49 of 100 968s /usr/bin/bowtie2 --cp-min 8 --cp-ival 1 --mm --local -i C,4.92212594644199,7.0682291001079 --mp 8.34743664997263,7.88489855929109 --rdg 25.7207668830013,4.43876864588602 --score-min L,6.69272418826891,7.78554610943954 --gbar 2 --large-index -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 969s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '40' because it was < 2 characters long 969s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '47' because it was < 2 characters long 969s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '56' because it was < 2 characters long 969s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '72' because it was < 2 characters long 969s Warning: skipping read '73' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '73' because it was < 2 characters long 969s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '74' because it was < 2 characters long 969s Warning: skipping read '97' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '97' because it was < 2 characters long 969s 108 reads; of these: 969s 108 (100.00%) were unpaired; of these: 969s 108 (100.00%) aligned 0 times 969s 0 (0.00%) aligned exactly 1 time 969s 0 (0.00%) aligned >1 times 969s 0.00% overall alignment rate 969s Read 50 alignments... 969s Read 100 alignments... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s --- Summary --- 969s Read 1 reference strings 969s Checked 0 alignments, 0 edits 969s --------------- 969s PASSED 969s Flattened IUPAC characters 969s Mutating sequence Sim.pm.1 969s Introducing 3 SNPs, 0/1 ref/read gaps, and 1 rearrangements 969s Finished SNPs 969s Finished ref gaps 969s Finished read gaps 969s Mutating sequence Sim.pm.2 969s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 969s Finished SNPs 969s Finished ref gaps 969s Finished read gaps 969s Mutated reference genome to subject genome 969s SNPs introduced: 3 969s Reference gaps introduced: 1 969s Read gaps introduced: 1 969s Rearrangements introduced: 2 969s Created read sampler 969s Sampling 144 reads 969s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 969s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 969s parsing sequence Sim.pm.1... 969s parsing sequence Sim.pm.2... 969s Parsed 110 reference bases 969s *** Run 50 of 100 969s /usr/bin/bowtie2 --rdg 19.227166287745,17.0602775747532 -i C,4.45200548899382 --rfg 43.7893724749315 --large-index --score-min L,1.03359171462026,8.49263312475468 --cp-min 3 --np 2 --cp-ival 1 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 969s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 969s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '81' because it was < 2 characters long 969s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 969s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '88' because it was < 2 characters long 969s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 969s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '124' because it was < 2 characters long 969s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 969s 144 reads; of these: 969s 144 (100.00%) were unpaired; of these: 969s 109 (75.69%) aligned 0 times 969s 22 (15.28%) aligned exactly 1 time 969s 13 (9.03%) aligned >1 times 969s 24.31% overall alignment rate 969s Read 50 alignments... 969s Read 100 alignments... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s GGGCCTCGCAGCGGAAGC 969s GGGCCTCGCAGCGGAAGC 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s AGATGGGACAGGGGAGGCGAACAAAGGGCC 969s AGATGGGACAGGGGAGGCGAACAAAGGGCC 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s CACAGCATAGT 969s CACAGCATAGT 969s Processing line... 969s ATGTCCAGGGACG 969s ATGTCCAGGGACG 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s AA 969s AA 969s Processing line... 969s Processing line... 969s AGGGGAG 969s AGGGGAG 969s Processing line... 969s Processing line... 969s GAGGCGAACAAAGGGCC 969s GAGGCGAACAAAGGGCC 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s AAAGGGCCTCGC 969s AAAGGGCCTCGC 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s CA 969s CA 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s AGATGGGACAGGGGAGGCGAACAAAGGGCCTCGCAGCGGAAGC 969s AGATGGGACAGGGGAGGCGAACAAAGGGCCTCGCAGCGGAAGC 969s Processing line... 969s CAGCATAGTGCG 969s CAGCATAGTGCG 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s ATG 969s ATG 969s Processing line... 969s GGGCCTCGCAGCGGAAGC 969s GGGCCTCGCAGCGGAAGC 969s Processing line... 969s Processing line... 969s CGCA 969s CGCA 969s Processing line... 969s GACGCACAGCATAGTGCGACCGCGTC 969s GACGCACAGCATAGTGCGACCGCGTC 969s Processing line... 969s Processing line... 969s GGGACAGGGGAGGCGAAC 969s GGGACAGGGGAGGCGAAC 969s Processing line... 969s Processing line... 969s Processing line... 969s GGAGGCGA 969s GGAGGCGA 969s Processing line... 969s Processing line... 969s Processing line... 969s AGGGCCTCGCAGCG 969s AGGGCCTCGCAGCG 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s GGGACAGGGGAGGCGAACAAAGGGCCTCGC 969s GGGACAGGGGAGGCGAACAAAGGGCCTCGC 969s Processing line... 969s Processing line... 969s Processing line... 969s CAGCATAGTGC 969s CAGCATAGTGC 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s AG 969s AG 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s CAGGGAC 969s CAGGGAC 969s Processing line... 969s CGAA 969s CGAA 969s Processing line... 969s Processing line... 969s Processing line... 969s GCG 969s GCG 969s Processing line... 969s Processing line... 969s GGGAGGCGAACAAAGG 969s GGGAGGCGAACAAAGG 969s Processing line... 969s Processing line... 969s AT 969s AT 969s Processing line... 969s Processing line... 969s GGGACAGGGGAGGCGAACAAAGGGCCTCGC 969s GGGACAGGGGAGGCGAACAAAGGGCCTCGC 969s Processing line... 969s Processing line... 969s Processing line... 969s AT 969s AT 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s GAACAAAGGGCC 969s GAACAAAGGGCC 969s Processing line... 969s ATAG 969s ATAG 969s Processing line... 969s Processing line... 969s TG 969s TG 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s GGC 969s GGC 969s Processing line... 969s Processing line... 969s Processing line... 969s GGC 969s GGC 969s Processing line... 969s Processing line... 969s AC 969s AC 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s GCACAGCATA 969s GCACAGCATA 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s Processing line... 969s --- Summary --- 969s Read 1 reference strings 969s Checked 35 alignments, 0 edits 969s --------------- 969s PASSED 969s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 969s /usr/bin/bowtie2 --rdg 19.227166287745,17.0602775747532 -i C,4.45200548899382 --rfg 43.7893724749315 --large-index --score-min L,1.03359171462026,8.49263312475468 --cp-min 3 --np 2 --cp-ival 1 -q -p 4 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 969s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 969s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '81' because it was < 2 characters long 969s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 969s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '88' because it was < 2 characters long 969s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 969s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 969s Warning: skipping read '124' because it was < 2 characters long 969s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 969s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 969s 144 reads; of these: 969s 144 (100.00%) were unpaired; of these: 969s 109 (75.69%) aligned 0 times 969s 22 (15.28%) aligned exactly 1 time 969s 13 (9.03%) aligned >1 times 969s 24.31% overall alignment rate 969s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 969s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 969s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 969s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 969s /usr/bin/bowtie2 --rdg 19.227166287745,17.0602775747532 -i C,4.45200548899382 --rfg 43.7893724749315 --large-index --score-min L,1.03359171462026,8.49263312475468 --cp-min 3 --np 2 --cp-ival 1 -q -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 970s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 970s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 970s Warning: skipping read '81' because it was < 2 characters long 970s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 970s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 970s Warning: skipping read '88' because it was < 2 characters long 970s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 970s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 970s Warning: skipping read '124' because it was < 2 characters long 970s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 970s 144 reads; of these: 970s 144 (100.00%) were unpaired; of these: 970s 109 (75.69%) aligned 0 times 970s 22 (15.28%) aligned exactly 1 time 970s 13 (9.03%) aligned >1 times 970s 24.31% overall alignment rate 970s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 970s Flattened IUPAC characters 970s Mutating sequence Sim.pm.2 970s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 970s Finished SNPs 970s Finished ref gaps 970s Finished read gaps 970s Mutating sequence Sim.pm.1 970s Introducing 1 SNPs, 0/4 ref/read gaps, and 0 rearrangements 970s Finished SNPs 970s Finished ref gaps 970s Finished read gaps 970s Mutated reference genome to subject genome 970s SNPs introduced: 4 970s Reference gaps introduced: 1 970s Read gaps introduced: 5 970s Rearrangements introduced: 0 970s Created read sampler 970s Sampling 51 reads 970s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 970s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 970s parsing sequence Sim.pm.1... 970s parsing sequence Sim.pm.2... 970s Parsed 110 reference bases 970s *** Run 51 of 100 970s /usr/bin/bowtie2 -D 46 --trim5 2 -i L,0.0256868943960341,0.87630619038177 --score-min L,7.38965483434529,7.96313271944704 --cp-min 4 --cp-ival 1 --mp 9.93289602282278,1.56403621143805 --rdg 36.0247969343829,11.1486612267961 --large-index -M 3 -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 970s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 970s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 970s Warning: skipping read '18' because it was < 2 characters long 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 970s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 970s Warning: skipping mate #2 of read '23' because it was < 2 characters long 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 970s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 970s Warning: skipping mate #1 of read '50' because it was < 2 characters long 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 970s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 970s 51 reads; of these: 970s 49 (96.08%) were paired; of these: 970s 49 (100.00%) aligned concordantly 0 times 970s 0 (0.00%) aligned concordantly exactly 1 time 970s 0 (0.00%) aligned concordantly >1 times 970s ---- 970s 49 pairs aligned concordantly 0 times; of these: 970s 0 (0.00%) aligned discordantly 1 time 970s ---- 970s 49 pairs aligned 0 times concordantly or discordantly; of these: 970s 98 mates make up the pairs; of these: 970s 82 (83.67%) aligned 0 times 970s 11 (11.22%) aligned exactly 1 time 970s 5 (5.10%) aligned >1 times 970s 2 (3.92%) were unpaired; of these: 970s 1 (50.00%) aligned 0 times 970s 1 (50.00%) aligned exactly 1 time 970s 0 (0.00%) aligned >1 times 970s 17.00% overall alignment rate 970s Read 50 alignments... 970s Read 100 alignments... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s TCG 970s TCG 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s GGGA 970s GGGA 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s CATGTCCAGG 970s CATGTCCAGG 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s GAATGCAGATG 970s GAATGCAGATG 970s Processing line... 970s GC 970s GC 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s GC 970s GC 970s Processing line... 970s Processing line... 970s GGGACAGGGGAGGCGAACAAAGGGCCTCGCAGCGGA 970s GGGACAGGGGAGGCGAACAAAGGGCCTCGCAGCGGA 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s GCAGAT 970s GCAGAT 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s GGACG 970s GGACG 970s Processing line... 970s Processing line... 970s GGGACAGGGGAGGCGAACA 970s GGGACAGGGGAGGCGAACA 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s CA 970s CA 970s Processing line... 970s Processing line... 970s GCAGATGG 970s GCAGATGG 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s AGGGGAGGCGAACAAAGGG 970s AGGGGAGGCGAACAAAGGG 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s GAACAAAG 970s GAACAAAG 970s Processing line... 970s Processing line... 970s AGATGGG 970s AGATGGG 970s Processing line... 970s Processing line... 970s GGGACAGGGGA 970s GGGACAGGGGA 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s GGGCCTCG 970s GGGCCTCG 970s Processing line... 970s --- Summary --- 970s Read 1 reference strings 970s Checked 17 alignments, 0 edits 970s --------------- 970s PASSED 970s Flattened IUPAC characters 970s Mutating sequence Sim.pm.2 970s Introducing 15 SNPs, 1/2 ref/read gaps, and 0 rearrangements 970s Finished SNPs 970s Finished ref gaps 970s Finished read gaps 970s Mutating sequence Sim.pm.1 970s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 970s Finished SNPs 970s Finished ref gaps 970s Finished read gaps 970s Mutated reference genome to subject genome 970s SNPs introduced: 23 970s Reference gaps introduced: 2 970s Read gaps introduced: 2 970s Rearrangements introduced: 0 970s Created read sampler 970s Sampling 54 reads 970s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 970s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 970s parsing sequence Sim.pm.1... 970s parsing sequence Sim.pm.2... 970s Parsed 110 reference bases 970s *** Run 52 of 100 970s /usr/bin/bowtie2 --norc --nofw --np 2 -N 1 -L13 -D 27 -i S,1.11298303660171 --score-min L,2.00863215873657,8.25354379906842 --cp-min 3 --cp-ival 1 --mp 6.89701099146434,1.05279121477495 --local --large-index -r -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw 970s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (1) 970s Warning: skipping mate #2 of read '3' because it was < 2 characters long 970s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (1) 970s Warning: skipping mate #1 of read '12' because it was < 2 characters long 970s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (1) 970s Warning: skipping mate #2 of read '20' because it was < 2 characters long 970s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (1) 970s Warning: skipping mate #1 of read '31' because it was < 2 characters long 970s 54 reads; of these: 970s 54 (100.00%) were paired; of these: 970s 54 (100.00%) aligned concordantly 0 times 970s 0 (0.00%) aligned concordantly exactly 1 time 970s 0 (0.00%) aligned concordantly >1 times 970s ---- 970s 54 pairs aligned concordantly 0 times; of these: 970s 0 (0.00%) aligned discordantly 1 time 970s ---- 970s 54 pairs aligned 0 times concordantly or discordantly; of these: 970s 108 mates make up the pairs; of these: 970s 108 (100.00%) aligned 0 times 970s 0 (0.00%) aligned exactly 1 time 970s 0 (0.00%) aligned >1 times 970s 0.00% overall alignment rate 970s Read 50 alignments... 970s Read 100 alignments... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s Processing line... 970s --- Summary --- 970s Read 1 reference strings 970s Checked 0 alignments, 0 edits 970s --------------- 970s PASSED 970s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 970s /usr/bin/bowtie2 --norc --nofw --np 2 -N 1 -L13 -D 27 -i S,1.11298303660171 --score-min L,2.00863215873657,8.25354379906842 --cp-min 3 --cp-ival 1 --mp 6.89701099146434,1.05279121477495 --local --large-index -r -p 3 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 971s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #2 of read '3' because it was < 2 characters long 971s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #1 of read '12' because it was < 2 characters long 971s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #2 of read '20' because it was < 2 characters long 971s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #1 of read '31' because it was < 2 characters long 971s 54 reads; of these: 971s 54 (100.00%) were paired; of these: 971s 54 (100.00%) aligned concordantly 0 times 971s 0 (0.00%) aligned concordantly exactly 1 time 971s 0 (0.00%) aligned concordantly >1 times 971s ---- 971s 54 pairs aligned concordantly 0 times; of these: 971s 0 (0.00%) aligned discordantly 1 time 971s ---- 971s 54 pairs aligned 0 times concordantly or discordantly; of these: 971s 108 mates make up the pairs; of these: 971s 108 (100.00%) aligned 0 times 971s 0 (0.00%) aligned exactly 1 time 971s 0 (0.00%) aligned >1 times 971s 0.00% overall alignment rate 971s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 971s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 971s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 971s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 971s /usr/bin/bowtie2 --norc --nofw --np 2 -N 1 -L13 -D 27 -i S,1.11298303660171 --score-min L,2.00863215873657,8.25354379906842 --cp-min 3 --cp-ival 1 --mp 6.89701099146434,1.05279121477495 --local --large-index -r -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 971s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #2 of read '3' because it was < 2 characters long 971s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #1 of read '12' because it was < 2 characters long 971s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #2 of read '20' because it was < 2 characters long 971s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #1 of read '31' because it was < 2 characters long 971s 54 reads; of these: 971s 54 (100.00%) were paired; of these: 971s 54 (100.00%) aligned concordantly 0 times 971s 0 (0.00%) aligned concordantly exactly 1 time 971s 0 (0.00%) aligned concordantly >1 times 971s ---- 971s 54 pairs aligned concordantly 0 times; of these: 971s 0 (0.00%) aligned discordantly 1 time 971s ---- 971s 54 pairs aligned 0 times concordantly or discordantly; of these: 971s 108 mates make up the pairs; of these: 971s 108 (100.00%) aligned 0 times 971s 0 (0.00%) aligned exactly 1 time 971s 0 (0.00%) aligned >1 times 971s 0.00% overall alignment rate 971s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 971s Flattened IUPAC characters 971s Mutating sequence Sim.pm.1 971s Introducing 1 SNPs, 1/1 ref/read gaps, and 1 rearrangements 971s Finished SNPs 971s Finished ref gaps 971s Finished read gaps 971s Mutating sequence Sim.pm.2 971s Introducing 13 SNPs, 0/2 ref/read gaps, and 3 rearrangements 971s Finished SNPs 971s Finished ref gaps 971s Finished read gaps 971s Mutated reference genome to subject genome 971s SNPs introduced: 14 971s Reference gaps introduced: 1 971s Read gaps introduced: 3 971s Rearrangements introduced: 4 971s Created read sampler 971s Sampling 114 reads 971s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 971s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 971s parsing sequence Sim.pm.1... 971s parsing sequence Sim.pm.2... 971s Parsed 110 reference bases 971s *** Run 53 of 100 971s /usr/bin/bowtie2 --rfg 39.9366119655837,8.63721177641442 --mp 4.75028237829637,1.19541719863678 --score-min L,7.58618258071389,1.44518274340803 --large-index --np 3 --cp-min 4 -R 2 --cp-ival 1 -N 1 -L20 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s Read 50 alignments... 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s Read 100 alignments... 971s Read 150 alignments... 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s Warning: skipping mate #2 of read 'R_1_1_1_107_107_1/1' because length (1) <= # seed mismatches (1) 971s Warning: skipping mate #2 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 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 971s 114 reads; of these: 971s 114 (100.00%) were paired; of these: 971s 114 (100.00%) aligned concordantly 0 times 971s 0 (0.00%) aligned concordantly exactly 1 time 971s 0 (0.00%) aligned concordantly >1 times 971s ---- 971s 114 pairs aligned concordantly 0 times; of these: 971s 1 (0.88%) aligned discordantly 1 time 971s ---- 971s 113 pairs aligned 0 times concordantly or discordantly; of these: 971s 226 mates make up the pairs; of these: 971s 199 (88.05%) aligned 0 times 971s 18 (7.96%) aligned exactly 1 time 971s 9 (3.98%) aligned >1 times 971s 12.72% overall alignment rate 971s Read 200 alignments... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s GAGG 971s GAGG 971s Processing line... 971s Processing line... 971s GA 971s GA 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s ACAGCATAGTGCGACCGCGT 971s ACAGCATAGTGCGACCGCGT 971s Processing line... 971s Processing line... 971s TCG 971s TCG 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s TGGGACA 971s TGGGACA 971s Processing line... 971s Processing line... 971s GCAGATGGGACAGGGGA 971s GCAGATGGGACAGGGGA 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s GGGACAGG 971s GGGACAGG 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s CAGGGACGCACAG 971s CAGGGACGCACAG 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s GCC 971s GCC 971s Processing line... 971s Processing line... 971s GATGGGACAGG 971s GATGGGACAGG 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s GGAGG 971s GGAGG 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s GGACGCACAGC 971s GGACGCACAGC 971s Processing line... 971s Processing line... 971s GGAGG 971s GGAGG 971s Processing line... 971s Processing line... 971s CATA 971s CATA 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s AATGCAGATGG 971s AATGCAGATGG 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s CA 971s CA 971s Processing line... 971s Processing line... 971s GGACAGGGGA 971s GGACAGGGGA 971s Processing line... 971s Processing line... 971s ATAGTGCG 971s ATAGTGCG 971s Processing line... 971s GCGAC 971s GCGAC 971s Processing line... 971s Processing line... 971s Processing line... 971s GAGGCGAACAA 971s GAGGCGAACAA 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s ATGCAGA 971s ATGCAGA 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s GGGGAGG 971s GGGGAGG 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s GG 971s GG 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s GCA 971s GCA 971s Processing line... 971s Processing line... 971s GGGACGCACAGCATAGTGCGACCGCG 971s GGGACGCACAGCATAGTGCGACCGCG 971s Processing line... 971s Processing line... 971s CGA 971s CGA 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s Processing line... 971s GGCCTCGCAGCGG 971s GGCCTCGCAGCGG 971s Processing line... 971s Processing line... 971s CGGAA 971s CGGAA 971s Processing line... 971s Processing line... 971s TGC 971s TGC 971s Processing line... 971s Processing line... 971s Processing line... 971s --- Summary --- 971s /usr/bin/bowtie2 --rfg 39.9366119655837,8.63721177641442 --mp 4.75028237829637,1.19541719863678 --score-min L,7.58618258071389,1.44518274340803 --large-index --np 3 --cp-min 4 -R 2 --cp-ival 1 -N 1 -L20 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 971s Read 1 reference strings 971s Checked 29 alignments, 0 edits 971s --------------- 971s PASSED 971s ALSO checking that bowtie2 and bowtie2-align match up 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (1) 972s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (1) 972s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (1) 972s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (1) 972s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s Warning: skipping mate #2 of read 'R_1_1_1_107_107_1/1' because length (1) <= # seed mismatches (1) 972s Warning: skipping mate #2 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 114 reads; of these: 972s 114 (100.00%) were paired; of these: 972s 114 (100.00%) aligned concordantly 0 times 972s 0 (0.00%) aligned concordantly exactly 1 time 972s 0 (0.00%) aligned concordantly >1 times 972s ---- 972s 114 pairs aligned concordantly 0 times; of these: 972s 1 (0.88%) aligned discordantly 1 time 972s ---- 972s 113 pairs aligned 0 times concordantly or discordantly; of these: 972s 226 mates make up the pairs; of these: 972s 199 (88.05%) aligned 0 times 972s 18 (7.96%) aligned exactly 1 time 972s 9 (3.98%) aligned >1 times 972s 12.72% overall alignment rate 972s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 972s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 972s /usr/bin/bowtie2 --rfg 39.9366119655837,8.63721177641442 --mp 4.75028237829637,1.19541719863678 --score-min L,7.58618258071389,1.44518274340803 --large-index --np 3 --cp-min 4 -R 2 --cp-ival 1 -N 1 -L20 --qseq -p 3 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (1) 972s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (1) 972s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (1) 972s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (1) 972s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s Warning: skipping mate #2 of read 'R_1_1_1_107_107_1/1' because length (1) <= # seed mismatches (1) 972s Warning: skipping mate #2 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 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 972s 114 reads; of these: 972s 114 (100.00%) were paired; of these: 972s 114 (100.00%) aligned concordantly 0 times 972s 0 (0.00%) aligned concordantly exactly 1 time 972s 0 (0.00%) aligned concordantly >1 times 972s ---- 972s 114 pairs aligned concordantly 0 times; of these: 972s 1 (0.88%) aligned discordantly 1 time 972s ---- 972s 113 pairs aligned 0 times concordantly or discordantly; of these: 972s 226 mates make up the pairs; of these: 972s 199 (88.05%) aligned 0 times 972s 18 (7.96%) aligned exactly 1 time 972s 9 (3.98%) aligned >1 times 972s 12.72% overall alignment rate 972s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 972s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 972s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 972s Flattened IUPAC characters 972s Mutating sequence Sim.pm.2 972s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 972s Finished SNPs 972s Finished ref gaps 972s Finished read gaps 972s Mutating sequence Sim.pm.1 972s Introducing 11 SNPs, 0/0 ref/read gaps, and 1 rearrangements 972s Finished SNPs 972s Finished ref gaps 972s Finished read gaps 972s Mutated reference genome to subject genome 972s SNPs introduced: 11 972s Reference gaps introduced: 0 972s Read gaps introduced: 0 972s Rearrangements introduced: 1 972s Created read sampler 972s Sampling 77 reads 972s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 972s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 972s parsing sequence Sim.pm.1... 972s parsing sequence Sim.pm.2... 972s *** Run 54 of 100 972s /usr/bin/bowtie2 --np 6 --norc --score-min L,6.38313296649899,5.3921647599591 --n-ceil 0.0768325620008483,1.35105995197785 -i S,2.34528730593129 --trim5 9 --cp-ival 1 --cp-min 9 --large-index -M 13 --local --rdg 26.0504369797591 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 972s Parsed 110 reference bases 972s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 972s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '5' because it was < 2 characters long 972s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '6' because it was < 2 characters long 972s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '9' because it was < 2 characters long 972s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '13' because it was < 2 characters long 972s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '18' because it was < 2 characters long 972s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 972s Warning: skipping read '19' because it was < 2 characters long 972s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '20' because it was < 2 characters long 972s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '29' because it was < 2 characters long 972s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 972s Warning: skipping read '32' because it was < 2 characters long 972s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '33' because it was < 2 characters long 972s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '36' because it was < 2 characters long 972s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '43' because it was < 2 characters long 972s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '45' because it was < 2 characters long 972s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '48' because it was < 2 characters long 972s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '58' because it was < 2 characters long 972s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '60' because it was < 2 characters long 972s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '61' because it was < 2 characters long 972s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '73' because it was < 2 characters long 972s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 972s Warning: skipping read '76' because it was < 2 characters long 972s 77 reads; of these: 972s 77 (100.00%) were unpaired; of these: 972s 77 (100.00%) aligned 0 times 972s 0 (0.00%) aligned exactly 1 time 972s 0 (0.00%) aligned >1 times 972s 0.00% overall alignment rate 972s Read 50 alignments... 972s Processing line... 972s /usr/bin/bowtie2 --np 6 --norc --score-min L,6.38313296649899,5.3921647599591 --n-ceil 0.0768325620008483,1.35105995197785 -i S,2.34528730593129 --trim5 9 --cp-ival 1 --cp-min 9 --large-index -M 13 --local --rdg 26.0504369797591 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s Processing line... 972s --- Summary --- 972s Read 1 reference strings 972s Checked 0 alignments, 0 edits 972s --------------- 972s PASSED 972s ALSO checking that bowtie2 and bowtie2-align match up 973s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 973s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '5' because it was < 2 characters long 973s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '6' because it was < 2 characters long 973s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '9' because it was < 2 characters long 973s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '13' because it was < 2 characters long 973s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '18' because it was < 2 characters long 973s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 973s Warning: skipping read '19' because it was < 2 characters long 973s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '20' because it was < 2 characters long 973s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '29' because it was < 2 characters long 973s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 973s Warning: skipping read '32' because it was < 2 characters long 973s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '33' because it was < 2 characters long 973s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '36' because it was < 2 characters long 973s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '43' because it was < 2 characters long 973s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '45' because it was < 2 characters long 973s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '48' because it was < 2 characters long 973s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '58' because it was < 2 characters long 973s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '60' because it was < 2 characters long 973s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '61' because it was < 2 characters long 973s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '73' because it was < 2 characters long 973s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 973s Warning: skipping read '76' because it was < 2 characters long 973s 77 reads; of these: 973s 77 (100.00%) were unpaired; of these: 973s 77 (100.00%) aligned 0 times 973s 0 (0.00%) aligned exactly 1 time 973s 0 (0.00%) aligned >1 times 973s 0.00% overall alignment rate 973s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 973s Flattened IUPAC characters 973s Mutating sequence Sim.pm.1 973s Introducing 9 SNPs, 0/1 ref/read gaps, and 0 rearrangements 973s Finished SNPs 973s Finished ref gaps 973s Finished read gaps 973s Mutating sequence Sim.pm.2 973s Introducing 4 SNPs, 1/2 ref/read gaps, and 0 rearrangements 973s Finished SNPs 973s Finished ref gaps 973s Finished read gaps 973s Mutated reference genome to subject genome 973s SNPs introduced: 13 973s Reference gaps introduced: 1 973s Read gaps introduced: 3 973s Rearrangements introduced: 0 973s Created read sampler 973s Sampling 36 reads 973s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 973s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 973s parsing sequence Sim.pm.1... 973s parsing sequence Sim.pm.2... 973s Parsed 110 reference bases 973s *** Run 55 of 100 973s /usr/bin/bowtie2 --nofw --norc -i L,0.0129198728120835 --score-min L,8.30431209172426,6.57492469012206 --cp-min 3 --cp-ival 1 --mm --local -a --mp 7.20449219475586,3.03450520985431 --rdg 7.54846764431324 --large-index --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 973s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 973s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 973s 36 reads; of these: 973s 36 (100.00%) were paired; of these: 973s 36 (100.00%) aligned concordantly 0 times 973s 0 (0.00%) aligned concordantly exactly 1 time 973s 0 (0.00%) aligned concordantly >1 times 973s ---- 973s 36 pairs aligned concordantly 0 times; of these: 973s 0 (0.00%) aligned discordantly 1 time 973s ---- 973s 36 pairs aligned 0 times concordantly or discordantly; of these: 973s 72 mates make up the pairs; of these: 973s 72 (100.00%) aligned 0 times 973s 0 (0.00%) aligned exactly 1 time 973s 0 (0.00%) aligned >1 times 973s 0.00% overall alignment rate 973s Read 50 alignments... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s --- Summary --- 973s Read 1 reference strings 973s Checked 0 alignments, 0 edits 973s --------------- 973s PASSED 973s Flattened IUPAC characters 973s Mutating sequence Sim.pm.2 973s Introducing 12 SNPs, 1/0 ref/read gaps, and 1 rearrangements 973s Finished SNPs 973s Finished ref gaps 973s Finished read gaps 973s Mutating sequence Sim.pm.1 973s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 973s Finished SNPs 973s Finished ref gaps 973s Finished read gaps 973s Mutated reference genome to subject genome 973s SNPs introduced: 20 973s Reference gaps introduced: 1 973s Read gaps introduced: 0 973s Rearrangements introduced: 1 973s Created read sampler 973s Sampling 166 reads 973s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 973s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 973s parsing sequence Sim.pm.1... 973s parsing sequence Sim.pm.2... 973s *** Run 56 of 100 973s /usr/bin/bowtie2 --np 1 -R 3 -N 0 -L29 --score-min L,1.04360201242667,2.73688496818544 --n-ceil 1.05730251892037,1.28343888399764 --cp-min 2 --cp-ival 2 --local --rdg 18.2344159055154,18.6022477146196 -k 2 --large-index --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 973s Parsed 110 reference bases 973s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 973s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 973s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 973s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 973s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 973s Read 50 alignments... 973s Read 100 alignments... 973s Warning: skipping read 'R_1_1_1_142_142_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 973s Warning: skipping read 'R_1_1_1_160_160_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_160_160_1/1' because it was < 2 characters long 973s 166 reads; of these: 973s 166 (100.00%) were unpaired; of these: 973s 166 (100.00%) aligned 0 times 973s 0 (0.00%) aligned exactly 1 time 973s 0 (0.00%) aligned >1 times 973s 0.00% overall alignment rate 973s Read 150 alignments... 973s Processing line... 973s /usr/bin/bowtie2 --np 1 -R 3 -N 0 -L29 --score-min L,1.04360201242667,2.73688496818544 --n-ceil 1.05730251892037,1.28343888399764 --cp-min 2 --cp-ival 2 --local --rdg 18.2344159055154,18.6022477146196 -k 2 --large-index --qseq -p 2 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s Processing line... 973s --- Summary --- 973s Read 1 reference strings 973s Checked 0 alignments, 0 edits 973s --------------- 973s PASSED 973s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 973s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 973s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 973s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 973s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 973s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 974s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (1) <= # seed mismatches (0) 974s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 974s Warning: skipping read 'R_1_1_1_142_142_1/1' because length (1) <= # seed mismatches (0) 974s Warning: skipping read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 974s Warning: skipping read 'R_1_1_1_160_160_1/1' because length (1) <= # seed mismatches (0) 974s Warning: skipping read 'R_1_1_1_160_160_1/1' because it was < 2 characters long 974s 166 reads; of these: 974s 166 (100.00%) were unpaired; of these: 974s 166 (100.00%) aligned 0 times 974s 0 (0.00%) aligned exactly 1 time 974s 0 (0.00%) aligned >1 times 974s 0.00% overall alignment rate 974s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 974s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 974s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 974s Flattened IUPAC characters 974s Mutating sequence Sim.pm.2 974s Introducing 12 SNPs, 0/1 ref/read gaps, and 2 rearrangements 974s Finished SNPs 974s Finished ref gaps 974s Finished read gaps 974s Mutating sequence Sim.pm.1 974s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 974s Finished SNPs 974s Finished ref gaps 974s Finished read gaps 974s Mutated reference genome to subject genome 974s SNPs introduced: 19 974s Reference gaps introduced: 0 974s Read gaps introduced: 1 974s Rearrangements introduced: 2 974s Created read sampler 974s Sampling 185 reads 974s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 974s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 974s parsing sequence Sim.pm.1... 974s parsing sequence Sim.pm.2... 974s Parsed 110 reference bases 974s *** Run 57 of 100 974s /usr/bin/bowtie2 --mm --cp-ival 4 --cp-min 2 --large-index --local --trim3 2 -R 1 -N 1 -L30 --np 4 --score-min L,2.31836559207229,3.04015302444483 --trim5 5 -f -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta 974s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '1' because it was < 2 characters long 974s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '4' because it was < 2 characters long 974s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '13' because it was < 2 characters long 974s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '15' because it was < 2 characters long 974s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '34' because it was < 2 characters long 974s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '36' because it was < 2 characters long 974s Warning: skipping read '42' because length (1) <= # seed mismatches (1) 974s Warning: skipping read '42' because it was < 2 characters long 974s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '44' because it was < 2 characters long 974s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '45' because it was < 2 characters long 974s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '52' because it was < 2 characters long 974s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '55' because it was < 2 characters long 974s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '63' because it was < 2 characters long 974s Warning: skipping read '66' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '66' because it was < 2 characters long 974s Warning: skipping read '69' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '69' because it was < 2 characters long 974s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '70' because it was < 2 characters long 974s Warning: skipping read '72' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '72' because it was < 2 characters long 974s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '75' because it was < 2 characters long 974s Warning: skipping read '78' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '78' because it was < 2 characters long 974s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '82' because it was < 2 characters long 974s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '88' because it was < 2 characters long 974s Warning: skipping read '98' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '98' because it was < 2 characters long 974s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '100' because it was < 2 characters long 974s Warning: skipping read '103' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '103' because it was < 2 characters long 974s Warning: skipping read '104' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '104' because it was < 2 characters long 974s Warning: skipping read '108' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '108' because it was < 2 characters long 974s Warning: skipping read '112' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '112' because it was < 2 characters long 974s Warning: skipping read '113' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '113' because it was < 2 characters long 974s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '119' because it was < 2 characters long 974s Warning: skipping read '120' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '120' because it was < 2 characters long 974s Warning: skipping read '122' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '122' because it was < 2 characters long 974s Warning: skipping read '124' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '124' because it was < 2 characters long 974s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '126' because it was < 2 characters long 974s Warning: skipping read '130' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '130' because it was < 2 characters long 974s Warning: skipping read '133' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '133' because it was < 2 characters long 974s Warning: skipping read '134' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '134' because it was < 2 characters long 974s Warning: skipping read '135' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '135' because it was < 2 characters long 974s Warning: skipping read '137' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '137' because it was < 2 characters long 974s Warning: skipping read '140' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '140' because it was < 2 characters long 974s Warning: skipping read '142' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '142' because it was < 2 characters long 974s Warning: skipping read '143' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '143' because it was < 2 characters long 974s Warning: skipping read '146' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '146' because it was < 2 characters long 974s Warning: skipping read '147' because length (1) <= # seed mismatches (1) 974s Warning: skipping read '147' because it was < 2 characters long 974s Warning: skipping read '151' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '151' because it was < 2 characters long 974s Warning: skipping read '154' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '154' because it was < 2 characters long 974s Warning: skipping read '164' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '164' because it was < 2 characters long 974s Warning: skipping read '167' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '167' because it was < 2 characters long 974s Warning: skipping read '172' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '172' because it was < 2 characters long 974s Warning: skipping read '173' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '173' because it was < 2 characters long 974s Warning: skipping read '176' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '176' because it was < 2 characters long 974s Warning: skipping read '177' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '177' because it was < 2 characters long 974s Warning: skipping read '180' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '180' because it was < 2 characters long 974s Warning: skipping read '181' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '181' because it was < 2 characters long 974s Warning: skipping read '184' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '184' because it was < 2 characters long 974s Warning: skipping read '185' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '185' because it was < 2 characters long 974s 185 reads; of these: 974s 185 (100.00%) were unpaired; of these: 974s 185 (100.00%) aligned 0 times 974s 0 (0.00%) aligned exactly 1 time 974s 0 (0.00%) aligned >1 times 974s 0.00% overall alignment rate 974s Read 50 alignments... 974s Read 100 alignments... 974s Read 150 alignments... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s /usr/bin/bowtie2 --mm --cp-ival 4 --cp-min 2 --large-index --local --trim3 2 -R 1 -N 1 -L30 --np 4 --score-min L,2.31836559207229,3.04015302444483 --trim5 5 -f -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s --- Summary --- 974s Read 1 reference strings 974s Checked 0 alignments, 0 edits 974s --------------- 974s PASSED 974s ALSO checking that bowtie2 and bowtie2-align match up 974s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '1' because it was < 2 characters long 974s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '4' because it was < 2 characters long 974s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '13' because it was < 2 characters long 974s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '15' because it was < 2 characters long 974s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '34' because it was < 2 characters long 974s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '36' because it was < 2 characters long 974s Warning: skipping read '42' because length (1) <= # seed mismatches (1) 974s Warning: skipping read '42' because it was < 2 characters long 974s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '44' because it was < 2 characters long 974s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '45' because it was < 2 characters long 974s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '52' because it was < 2 characters long 974s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '55' because it was < 2 characters long 974s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '63' because it was < 2 characters long 974s Warning: skipping read '66' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '66' because it was < 2 characters long 974s Warning: skipping read '69' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '69' because it was < 2 characters long 974s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '70' because it was < 2 characters long 974s Warning: skipping read '72' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '72' because it was < 2 characters long 974s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '75' because it was < 2 characters long 974s Warning: skipping read '78' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '78' because it was < 2 characters long 974s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '82' because it was < 2 characters long 974s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '88' because it was < 2 characters long 974s Warning: skipping read '98' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '98' because it was < 2 characters long 974s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '100' because it was < 2 characters long 974s Warning: skipping read '103' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '103' because it was < 2 characters long 974s Warning: skipping read '104' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '104' because it was < 2 characters long 974s Warning: skipping read '108' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '108' because it was < 2 characters long 974s Warning: skipping read '112' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '112' because it was < 2 characters long 974s Warning: skipping read '113' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '113' because it was < 2 characters long 974s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '119' because it was < 2 characters long 974s Warning: skipping read '120' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '120' because it was < 2 characters long 974s Warning: skipping read '122' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '122' because it was < 2 characters long 974s Warning: skipping read '124' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '124' because it was < 2 characters long 974s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '126' because it was < 2 characters long 974s Warning: skipping read '130' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '130' because it was < 2 characters long 974s Warning: skipping read '133' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '133' because it was < 2 characters long 974s Warning: skipping read '134' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '134' because it was < 2 characters long 974s Warning: skipping read '135' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '135' because it was < 2 characters long 974s Warning: skipping read '137' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '137' because it was < 2 characters long 974s Warning: skipping read '140' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '140' because it was < 2 characters long 974s Warning: skipping read '142' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '142' because it was < 2 characters long 974s Warning: skipping read '143' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '143' because it was < 2 characters long 974s Warning: skipping read '146' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '146' because it was < 2 characters long 974s Warning: skipping read '147' because length (1) <= # seed mismatches (1) 974s Warning: skipping read '147' because it was < 2 characters long 974s Warning: skipping read '151' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '151' because it was < 2 characters long 974s Warning: skipping read '154' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '154' because it was < 2 characters long 974s Warning: skipping read '164' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '164' because it was < 2 characters long 974s Warning: skipping read '167' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '167' because it was < 2 characters long 974s Warning: skipping read '172' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '172' because it was < 2 characters long 974s Warning: skipping read '173' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '173' because it was < 2 characters long 974s Warning: skipping read '176' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '176' because it was < 2 characters long 974s Warning: skipping read '177' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '177' because it was < 2 characters long 974s Warning: skipping read '180' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '180' because it was < 2 characters long 974s Warning: skipping read '181' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '181' because it was < 2 characters long 974s Warning: skipping read '184' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '184' because it was < 2 characters long 974s Warning: skipping read '185' because length (0) <= # seed mismatches (1) 974s Warning: skipping read '185' because it was < 2 characters long 974s 185 reads; of these: 974s 185 (100.00%) were unpaired; of these: 974s 185 (100.00%) aligned 0 times 974s 0 (0.00%) aligned exactly 1 time 974s 0 (0.00%) aligned >1 times 974s 0.00% overall alignment rate 974s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 974s Flattened IUPAC characters 974s Mutating sequence Sim.pm.1 974s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 974s Finished SNPs 974s Finished ref gaps 974s Finished read gaps 974s Mutating sequence Sim.pm.2 974s Introducing 6 SNPs, 3/0 ref/read gaps, and 1 rearrangements 974s Finished SNPs 974s Finished ref gaps 974s Finished read gaps 974s Mutated reference genome to subject genome 974s SNPs introduced: 16 974s Reference gaps introduced: 3 974s Read gaps introduced: 0 974s Rearrangements introduced: 2 974s Created read sampler 974s Sampling 134 reads 974s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 974s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 974s parsing sequence Sim.pm.1... 974s parsing sequence Sim.pm.2... 974s *** Run 58 of 100 974s /usr/bin/bowtie2 --score-min L,1.86104111242504,2.85250054880164 --ma 9.70820300057403 --large-index -i S,2.34886322992545 --trim5 5 --trim3 9 --cp-ival 1 -N 0 -L24 --norc --np 2 --cp-min 2 -f -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta 974s Parsed 110 reference bases 974s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 974s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 974s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '2' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 974s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '6' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 974s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '7' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 974s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '8' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 974s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '12' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 974s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '14' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 974s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '20' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 974s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '21' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 974s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '22' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 974s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '23' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 974s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '24' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 974s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '25' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 974s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '28' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 974s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '29' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 974s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '40' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 974s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '45' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 974s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '46' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 974s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '48' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 974s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '49' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 974s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '50' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 974s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '51' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 974s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '56' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 974s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '57' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 974s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '59' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 974s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '61' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 974s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '64' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 974s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '67' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 974s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '70' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 974s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '74' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 974s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '76' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 974s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '78' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 974s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '80' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 974s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '83' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 974s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '85' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 974s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '86' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 974s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '88' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 974s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '89' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 974s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '96' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 974s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '97' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 974s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '98' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 974s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '103' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 974s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '105' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 974s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '107' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 974s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '109' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 974s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '120' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 974s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '122' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 974s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '126' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 974s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '127' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 974s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '129' because it was < 2 characters long 974s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 974s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 974s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 974s Warning: skipping read '134' because it was < 2 characters long 974s 134 reads; of these: 974s 134 (100.00%) were unpaired; of these: 974s 124 (92.54%) aligned 0 times 974s 5 (3.73%) aligned exactly 1 time 974s 5 (3.73%) aligned >1 times 974s 7.46% overall alignment rate 974s Read 50 alignments... 974s Read 100 alignments... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s TGGG 974s TGGG 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s /usr/bin/bowtie2 --score-min L,1.86104111242504,2.85250054880164 --ma 9.70820300057403 --large-index -i S,2.34886322992545 --trim5 5 --trim3 9 --cp-ival 1 -N 0 -L24 --norc --np 2 --cp-min 2 -f -p 2 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s CA 974s CA 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s CA 974s CA 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s GCGA 974s GCGA 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s ATGCAGATGGGACAGGGGAGGCGA 974s ATGCAGATGGGACAGGGGAGGCGA 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s GAA 974s GAA 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s AT 974s AT 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s GTGCG 974s GTGCG 974s Processing line... 974s Processing line... 974s Processing line... 974s AAGGGCC 974s AAGGGCC 974s Processing line... 974s GGGAGGCGAAC 974s GGGAGGCGAAC 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s Processing line... 974s --- Summary --- 974s Read 1 reference strings 974s Checked 10 alignments, 0 edits 974s --------------- 974s PASSED 974s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 975s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 975s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 975s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '2' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 975s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '6' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 975s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '7' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 975s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '8' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 975s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '12' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 975s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '14' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 975s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '20' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 975s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '21' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 975s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '22' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 975s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '23' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 975s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '24' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 975s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '25' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 975s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '28' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 975s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '29' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 975s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '40' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 975s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '45' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 975s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '46' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 975s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '48' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 975s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '49' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 975s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '50' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 975s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '51' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 975s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '56' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 975s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '57' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 975s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '59' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 975s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '61' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 975s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '67' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 975s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '70' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 975s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '74' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 975s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '76' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 975s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '78' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 975s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '80' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 975s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '83' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 975s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '64' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 975s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '97' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 975s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '98' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 975s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '103' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 975s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '105' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 975s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '107' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 975s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '109' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 975s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '120' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 975s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '122' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 975s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '126' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 975s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '127' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 975s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '129' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 975s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '134' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 975s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '85' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 975s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '86' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 975s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '88' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 975s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '89' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 975s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '96' because it was < 2 characters long 975s 134 reads; of these: 975s 134 (100.00%) were unpaired; of these: 975s 124 (92.54%) aligned 0 times 975s 5 (3.73%) aligned exactly 1 time 975s 5 (3.73%) aligned >1 times 975s 7.46% overall alignment rate 975s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 975s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 975s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 975s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 975s /usr/bin/bowtie2 --score-min L,1.86104111242504,2.85250054880164 --ma 9.70820300057403 --large-index -i S,2.34886322992545 --trim5 5 --trim3 9 --cp-ival 1 -N 0 -L24 --norc --np 2 --cp-min 2 -f -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 975s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 975s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 975s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '2' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 975s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '6' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 975s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '7' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 975s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '8' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 975s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '12' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 975s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '14' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 975s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '20' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 975s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '21' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 975s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '22' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 975s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '23' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 975s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '24' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 975s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '25' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 975s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '28' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 975s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '29' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 975s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '40' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 975s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '45' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 975s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '46' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 975s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '48' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 975s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '49' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 975s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '50' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 975s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '51' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 975s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '56' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 975s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '57' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 975s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '59' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 975s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '61' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 975s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '64' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 975s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '83' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 975s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '85' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 975s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '86' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 975s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '88' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 975s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '89' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 975s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '96' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 975s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '97' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 975s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '98' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 975s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '103' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 975s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '105' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 975s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '107' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 975s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '109' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 975s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '67' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 975s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '70' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 975s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '74' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 975s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '76' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 975s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '78' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 975s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '80' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 975s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '129' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 975s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '134' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 975s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '120' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 975s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '122' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 975s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '126' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 975s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 975s Warning: skipping read '127' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 975s 134 reads; of these: 975s 134 (100.00%) were unpaired; of these: 975s 124 (92.54%) aligned 0 times 975s 5 (3.73%) aligned exactly 1 time 975s 5 (3.73%) aligned >1 times 975s 7.46% overall alignment rate 975s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 975s Flattened IUPAC characters 975s Mutating sequence Sim.pm.2 975s Introducing 2 SNPs, 0/0 ref/read gaps, and 3 rearrangements 975s Finished SNPs 975s Finished ref gaps 975s Finished read gaps 975s Mutating sequence Sim.pm.1 975s Introducing 8 SNPs, 3/1 ref/read gaps, and 0 rearrangements 975s Finished SNPs 975s Finished ref gaps 975s Finished read gaps 975s Mutated reference genome to subject genome 975s SNPs introduced: 10 975s Reference gaps introduced: 3 975s Read gaps introduced: 1 975s Rearrangements introduced: 3 975s Created read sampler 975s Sampling 107 reads 975s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 975s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 975s parsing sequence Sim.pm.1... 975s parsing sequence Sim.pm.2... 975s Parsed 110 reference bases 975s *** Run 59 of 100 975s /usr/bin/bowtie2 --mp 8.1901238947923,1.78195099228333 --trim5 0 --score-min L,3.01786032529461,4.82821577479986 -k 2 --large-index --norc --cp-min 4 --cp-ival 3 --mm -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 975s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 975s Warning: skipping mate #2 of read '13' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 975s Read 50 alignments... 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 975s Warning: skipping mate #2 of read '69' because length (1) <= # seed mismatches (0) 975s Warning: skipping mate #2 of read '69' because it was < 2 characters long 975s Read 100 alignments... 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 975s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 975s Warning: skipping mate #1 of read '85' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 975s Warning: skipping mate #1 of read '94' because length (1) <= # seed mismatches (0) 975s Warning: skipping mate #1 of read '94' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 975s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 975s Warning: skipping mate #2 of read '97' because it was < 2 characters long 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 975s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 975s 107 reads; of these: 975s 107 (100.00%) were paired; of these: 975s 107 (100.00%) aligned concordantly 0 times 975s 0 (0.00%) aligned concordantly exactly 1 time 975s 0 (0.00%) aligned concordantly >1 times 975s ---- 975s 107 pairs aligned concordantly 0 times; of these: 975s 0 (0.00%) aligned discordantly 1 time 975s ---- 975s 107 pairs aligned 0 times concordantly or discordantly; of these: 975s 214 mates make up the pairs; of these: 975s 182 (85.05%) aligned 0 times 975s 27 (12.62%) aligned exactly 1 time 975s 5 (2.34%) aligned >1 times 975s 14.95% overall alignment rate 975s Read 150 alignments... 975s Read 200 alignments... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s TCC 975s TCC 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s GGGACAGGGGAGGC 975s GGGACAGGGGAGGC 975s Processing line... 975s Processing line... 975s CTCGCAGCGGAAGC 975s CTCGCAGCGGAAGC 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s TCCAGGGACG 975s TCCAGGGACG 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s CC 975s CC 975s Processing line... 975s CC 975s CC 975s Processing line... 975s Processing line... 975s ATGCAGATGGGA 975s ATGCAGATGGGA 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s GCACAG 975s GCACAG 975s Processing line... 975s Processing line... 975s GCGGAAGC 975s GCGGAAGC 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s AAGC 975s AAGC 975s Processing line... 975s Processing line... 975s TGCG 975s TGCG 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s GAATGC 975s GAATGC 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s GCAGATGG 975s GCAGATGG 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s GA 975s GA 975s Processing line... 975s GA 975s GA 975s Processing line... 975s Processing line... 975s GGCGAAC 975s GGCGAAC 975s Processing line... 975s Processing line... 975s CAGGGG 975s CAGGGG 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s GGGACAGG 975s GGGACAGG 975s Processing line... 975s Processing line... 975s GGA 975s GGA 975s Processing line... 975s GGA 975s GGA 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s CGAACAAAGGG 975s CGAACAAAGGG 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s ATGGGACAGGG 975s ATGGGACAGGG 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s CGAACAAAGG 975s CGAACAAAGG 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s GCGGAAGC 975s GCGGAAGC 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s TGGGACAGGGGAGGCGAACAAAGGGC 975s TGGGACAGGGGAGGCGAACAAAGGGC 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s AGGGGAGGCGA 975s AGGGGAGGCGA 975s Processing line... 975s Processing line... 975s GAATGCAGATGGGACAG 975s GAATGCAGATGGGACAG 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s GGGACGCACAGCATAGT 975s GGGACGCACAGCATAGT 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s GGCCT 975s GGCCT 975s Processing line... 975s Processing line... 975s AGTGCGAC 975s AGTGCGAC 975s Processing line... 975s Processing line... 975s GA 975s GA 975s Processing line... 975s GA 975s GA 975s Processing line... 975s Processing line... 975s AGATGGGACAGGGG 975s AGATGGGACAGGGG 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s GACAGGGGAGGCGAACAAAGGGCCTCGCAGCGG 975s GACAGGGGAGGCGAACAAAGGGCCTCGCAGCGG 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s CGAA 975s CGAA 975s Processing line... 975s CGAA 975s CGAA 975s Processing line... 975s Processing line... 975s ATGGGACAGGGGAGGCGAACAAAGGGCC 975s ATGGGACAGGGGAGGCGAACAAAGGGCC 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s Processing line... 975s --- Summary --- 975s Read 1 reference strings 975s Checked 37 alignments, 0 edits 975s --------------- 975s PASSED 975s Flattened IUPAC characters 975s Mutating sequence Sim.pm.2 975s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 975s Finished SNPs 975s Finished ref gaps 975s Finished read gaps 975s Mutating sequence Sim.pm.1 975s Introducing 5 SNPs, 2/1 ref/read gaps, and 0 rearrangements 975s Finished SNPs 975s Finished ref gaps 975s Finished read gaps 975s Mutated reference genome to subject genome 975s SNPs introduced: 13 975s Reference gaps introduced: 3 975s Read gaps introduced: 1 975s Rearrangements introduced: 0 975s Created read sampler 975s Sampling 36 reads 975s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 975s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 975s parsing sequence Sim.pm.1... 975s parsing sequence Sim.pm.2... 975s Parsed 110 reference bases 975s *** Run 60 of 100 975s /usr/bin/bowtie2 --rfg 34.6091270645968 --trim5 5 --score-min L,8.93560052687584,5.01459061784679 --ma 21.4654834808624 --large-index --cp-min 4 --cp-ival 2 --mm -N 0 -L26 -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 976s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 976s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 976s Warning: skipping mate #1 of read '4' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 976s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 976s Warning: skipping read '8' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 976s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 976s Warning: skipping mate #1 of read '11' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 976s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 976s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 976s Warning: skipping mate #1 of read '18' because it was < 2 characters long 976s Warning: skipping mate #2 of read '18' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 976s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 976s Warning: skipping mate #1 of read '22' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 976s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 976s Warning: skipping mate #1 of read '26' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 976s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 976s Warning: skipping read '35' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 976s 36 reads; of these: 976s 33 (91.67%) were paired; of these: 976s 33 (100.00%) aligned concordantly 0 times 976s 0 (0.00%) aligned concordantly exactly 1 time 976s 0 (0.00%) aligned concordantly >1 times 976s ---- 976s 33 pairs aligned concordantly 0 times; of these: 976s 0 (0.00%) aligned discordantly 1 time 976s ---- 976s 33 pairs aligned 0 times concordantly or discordantly; of these: 976s 66 mates make up the pairs; of these: 976s 61 (92.42%) aligned 0 times 976s 2 (3.03%) aligned exactly 1 time 976s 3 (4.55%) aligned >1 times 976s 3 (8.33%) were unpaired; of these: 976s 3 (100.00%) aligned 0 times 976s 0 (0.00%) aligned exactly 1 time 976s 0 (0.00%) aligned >1 times 976s 7.25% overall alignment rate 976s Read 50 alignments... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s CACAGCATAGTGCGACCG 976s CACAGCATAGTGCGACCG 976s Processing line... 976s Processing line... 976s AT 976s AT 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s /usr/bin/bowtie2 --rfg 34.6091270645968 --trim5 5 --score-min L,8.93560052687584,5.01459061784679 --ma 21.4654834808624 --large-index --cp-min 4 --cp-ival 2 --mm -N 0 -L26 -q -p 4 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 976s Processing line... 976s CGTC 976s CGTC 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s AG 976s AG 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GGACAGGGGAGGCGAACAAAGGGCC 976s GGACAGGGGAGGCGAACAAAGGGCC 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s --- Summary --- 976s Read 1 reference strings 976s Checked 5 alignments, 0 edits 976s --------------- 976s PASSED 976s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 976s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 976s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 976s Warning: skipping mate #1 of read '4' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 976s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 976s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 976s Warning: skipping mate #1 of read '18' because it was < 2 characters long 976s Warning: skipping mate #2 of read '18' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 976s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 976s Warning: skipping read '8' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 976s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 976s Warning: skipping mate #1 of read '11' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 976s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 976s Warning: skipping mate #1 of read '22' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 976s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 976s Warning: skipping mate #1 of read '26' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 976s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 976s Warning: skipping read '35' because it was < 2 characters long 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 976s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 976s 36 reads; of these: 976s 33 (91.67%) were paired; of these: 976s 33 (100.00%) aligned concordantly 0 times 976s 0 (0.00%) aligned concordantly exactly 1 time 976s 0 (0.00%) aligned concordantly >1 times 976s ---- 976s 33 pairs aligned concordantly 0 times; of these: 976s 0 (0.00%) aligned discordantly 1 time 976s ---- 976s 33 pairs aligned 0 times concordantly or discordantly; of these: 976s 66 mates make up the pairs; of these: 976s 61 (92.42%) aligned 0 times 976s 2 (3.03%) aligned exactly 1 time 976s 3 (4.55%) aligned >1 times 976s 3 (8.33%) were unpaired; of these: 976s 3 (100.00%) aligned 0 times 976s 0 (0.00%) aligned exactly 1 time 976s 0 (0.00%) aligned >1 times 976s 7.25% overall alignment rate 976s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 976s Flattened IUPAC characters 976s Mutating sequence Sim.pm.2 976s Introducing 13 SNPs, 0/0 ref/read gaps, and 1 rearrangements 976s Finished SNPs 976s Finished ref gaps 976s Finished read gaps 976s Mutating sequence Sim.pm.1 976s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 976s Finished SNPs 976s Finished ref gaps 976s Finished read gaps 976s Mutated reference genome to subject genome 976s SNPs introduced: 18 976s Reference gaps introduced: 1 976s Read gaps introduced: 0 976s Rearrangements introduced: 1 976s Created read sampler 976s Sampling 127 reads 976s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 976s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 976s parsing sequence Sim.pm.1... 976s *** Run 61 of 100 976s /usr/bin/bowtie2 --mm -D 15 --cp-ival 2 --np 1 --cp-min 8 --score-min L,5.48809782904029,5.71125552824546 --large-index -M 7 --rdg 1.38417790860642,18.9103697242129 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 976s parsing sequence Sim.pm.2... 976s Parsed 110 reference bases 976s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 976s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 976s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 976s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 976s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 976s 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 976s 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 976s 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 976s 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 976s 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 976s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (1) <= # seed mismatches (0) 976s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (1) <= # seed mismatches (0) 976s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 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 976s 127 reads; of these: 976s 127 (100.00%) were unpaired; of these: 976s 102 (80.31%) aligned 0 times 976s 16 (12.60%) aligned exactly 1 time 976s 9 (7.09%) aligned >1 times 976s 19.69% overall alignment rate 976s Read 50 alignments... 976s Read 100 alignments... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s AATGCAGATGGGACAGG 976s AATGCAGATGGGACAGG 976s Processing line... 976s TCGGGAA 976s TCGGGAA 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GGGACGCACAGCATAGTGC 976s GGGACGCACAGCATAGTGC 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s AGC 976s AGC 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GCATGTCCAGGGACGCAC 976s GCATGTCCAGGGACGCAC 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GAGGCGAACAAAG 976s GAGGCGAACAAAG 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GGAAGA 976s GGAAGA 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GTGCGACCGCGT 976s GTGCGACCGCGT 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s CATAGT 976s CATAGT 976s Processing line... 976s Processing line... 976s GCTCGGGAAG 976s GCTCGGGAAG 976s Processing line... 976s Processing line... 976s Processing line... 976s TGG 976s TGG 976s Processing line... 976s GGACGCACAGCA 976s GGACGCACAGCA 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GC 976s GC 976s Processing line... 976s Processing line... 976s Processing line... 976s AA 976s AA 976s Processing line... 976s TCGGGAA 976s TCGGGAA 976s Processing line... 976s Processing line... 976s GGACGCACAGCA 976s GGACGCACAGCA 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GGA 976s GGA 976s Processing line... 976s Processing line... 976s GGGAC 976s GGGAC 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s CGG 976s CGG 976s Processing line... 976s CAGCATAG 976s CAGCATAG 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s CCAGGGACGCACAGCA 976s CCAGGGACGCACAGCA 976s Processing line... 976s GGACGCACAGCA 976s GGACGCACAGCA 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GCATGTCCAGGGACGCACAGCATAGTGCGACCGCGT 976s GCATGTCCAGGGACGCACAGCATAGTGCGACCGCGT 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GG 976s GG 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s GGC 976s GGC 976s Processing line... 976s Processing line... 976s Processing line... 976s Processing line... 976s --- Summary --- 976s Read 1 reference strings 976s Checked 25 alignments, 0 edits 976s --------------- 976s PASSED 976s Flattened IUPAC characters 976s Mutating sequence Sim.pm.1 976s Introducing 4 SNPs, 0/0 ref/read gaps, and 2 rearrangements 976s Finished SNPs 976s Finished ref gaps 976s Finished read gaps 976s Mutating sequence Sim.pm.2 976s Introducing 12 SNPs, 1/0 ref/read gaps, and 0 rearrangements 976s Finished SNPs 976s Finished ref gaps 976s Finished read gaps 976s Mutated reference genome to subject genome 976s SNPs introduced: 16 976s Reference gaps introduced: 1 976s Read gaps introduced: 0 976s Rearrangements introduced: 2 976s Created read sampler 976s Sampling 32 reads 976s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 976s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 976s *** Run 62 of 100 976s /usr/bin/bowtie2 -N 1 -L19 --nofw --score-min L,1.15417982177124,3.13678143947684 --gbar 4 --trim5 3 --rfg 21.0629520022082 -i C,0.605488597166972 --cp-ival 2 --mm --cp-min 3 --large-index -M 4 --local -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 976s parsing sequence Sim.pm.1... 976s parsing sequence Sim.pm.2... 976s Parsed 110 reference bases 976s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 976s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (1) 976s Warning: skipping mate #2 of read '8' because it was < 2 characters long 976s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (1) 976s Warning: skipping mate #2 of read '15' because it was < 2 characters long 976s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 976s Warning: skipping mate #1 of read '19' because it was < 2 characters long 976s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (1) 976s Warning: skipping mate #2 of read '22' because it was < 2 characters long 976s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (1) 976s Warning: skipping mate #2 of read '24' because it was < 2 characters long 977s 32 reads; of these: 977s 32 (100.00%) were paired; of these: 977s 32 (100.00%) aligned concordantly 0 times 977s 0 (0.00%) aligned concordantly exactly 1 time 977s 0 (0.00%) aligned concordantly >1 times 977s ---- 977s 32 pairs aligned concordantly 0 times; of these: 977s 0 (0.00%) aligned discordantly 1 time 977s ---- 977s 32 pairs aligned 0 times concordantly or discordantly; of these: 977s 64 mates make up the pairs; of these: 977s 64 (100.00%) aligned 0 times 977s 0 (0.00%) aligned exactly 1 time 977s 0 (0.00%) aligned >1 times 977s 0.00% overall alignment rate 977s Read 50 alignments... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s /usr/bin/bowtie2 -N 1 -L19 --nofw --score-min L,1.15417982177124,3.13678143947684 --gbar 4 --trim5 3 --rfg 21.0629520022082 -i C,0.605488597166972 --cp-ival 2 --mm --cp-min 3 --large-index -M 4 --local -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s --- Summary --- 977s Read 1 reference strings 977s Checked 0 alignments, 0 edits 977s --------------- 977s PASSED 977s ALSO checking that bowtie2 and bowtie2-align match up 977s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 977s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (1) 977s Warning: skipping mate #2 of read '8' because it was < 2 characters long 977s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (1) 977s Warning: skipping mate #2 of read '15' because it was < 2 characters long 977s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 977s Warning: skipping mate #1 of read '19' because it was < 2 characters long 977s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (1) 977s Warning: skipping mate #2 of read '22' because it was < 2 characters long 977s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (1) 977s Warning: skipping mate #2 of read '24' because it was < 2 characters long 977s 32 reads; of these: 977s 32 (100.00%) were paired; of these: 977s 32 (100.00%) aligned concordantly 0 times 977s 0 (0.00%) aligned concordantly exactly 1 time 977s 0 (0.00%) aligned concordantly >1 times 977s ---- 977s 32 pairs aligned concordantly 0 times; of these: 977s 0 (0.00%) aligned discordantly 1 time 977s ---- 977s 32 pairs aligned 0 times concordantly or discordantly; of these: 977s 64 mates make up the pairs; of these: 977s 64 (100.00%) aligned 0 times 977s 0 (0.00%) aligned exactly 1 time 977s 0 (0.00%) aligned >1 times 977s 0.00% overall alignment rate 977s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 977s Flattened IUPAC characters 977s Mutating sequence Sim.pm.1 977s Introducing 8 SNPs, 0/0 ref/read gaps, and 2 rearrangements 977s Finished SNPs 977s Finished ref gaps 977s Finished read gaps 977s Mutating sequence Sim.pm.2 977s Introducing 14 SNPs, 0/2 ref/read gaps, and 1 rearrangements 977s Finished SNPs 977s Finished ref gaps 977s Finished read gaps 977s Mutated reference genome to subject genome 977s SNPs introduced: 22 977s Reference gaps introduced: 0 977s Read gaps introduced: 2 977s Rearrangements introduced: 3 977s Created read sampler 977s Sampling 100 reads 977s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 977s *** Run 63 of 100 977s /usr/bin/bowtie2 --n-ceil 0.256390710265008,0.606668886759717 --score-min L,3.26721444014145,4.02066317608411 --trim5 5 -N 0 -L31 -R 1 --np 10 --large-index --rdg 1.36172802455112 -a --local --cp-ival 3 --cp-min 4 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 977s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 977s parsing sequence Sim.pm.1... 977s parsing sequence Sim.pm.2... 977s Parsed 110 reference bases 977s /usr/bin/bowtie2 --n-ceil 0.256390710265008,0.606668886759717 --score-min L,3.26721444014145,4.02066317608411 --trim5 5 -N 0 -L31 -R 1 --np 10 --large-index --rdg 1.36172802455112 -a --local --cp-ival 3 --cp-min 4 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 977s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 977s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 977s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 977s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 977s Read 50 alignments... 977s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 977s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 977s 100 reads; of these: 977s 87 (87.00%) were paired; of these: 977s 87 (100.00%) aligned concordantly 0 times 977s 0 (0.00%) aligned concordantly exactly 1 time 977s 0 (0.00%) aligned concordantly >1 times 977s ---- 977s 87 pairs aligned concordantly 0 times; of these: 977s 0 (0.00%) aligned discordantly 1 time 977s ---- 977s 87 pairs aligned 0 times concordantly or discordantly; of these: 977s 174 mates make up the pairs; of these: 977s 174 (100.00%) aligned 0 times 977s 0 (0.00%) aligned exactly 1 time 977s 0 (0.00%) aligned >1 times 977s 13 (13.00%) were unpaired; of these: 977s 13 (100.00%) aligned 0 times 977s 0 (0.00%) aligned exactly 1 time 977s 0 (0.00%) aligned >1 times 977s 0.00% overall alignment rate 977s Read 100 alignments... 977s Read 150 alignments... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s Processing line... 977s --- Summary --- 977s Read 1 reference strings 977s Checked 0 alignments, 0 edits 977s --------------- 977s PASSED 977s ALSO checking that bowtie2 and bowtie2-align match up 977s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 977s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 977s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 977s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 977s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 977s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 977s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 977s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 977s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 977s 100 reads; of these: 977s 87 (87.00%) were paired; of these: 977s 87 (100.00%) aligned concordantly 0 times 977s 0 (0.00%) aligned concordantly exactly 1 time 977s 0 (0.00%) aligned concordantly >1 times 977s ---- 977s 87 pairs aligned concordantly 0 times; of these: 977s 0 (0.00%) aligned discordantly 1 time 977s ---- 977s 87 pairs aligned 0 times concordantly or discordantly; of these: 977s 174 mates make up the pairs; of these: 977s 174 (100.00%) aligned 0 times 977s 0 (0.00%) aligned exactly 1 time 977s 0 (0.00%) aligned >1 times 977s 13 (13.00%) were unpaired; of these: 977s 13 (100.00%) aligned 0 times 977s 0 (0.00%) aligned exactly 1 time 977s 0 (0.00%) aligned >1 times 977s 0.00% overall alignment rate 977s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 977s Flattened IUPAC characters 977s Mutating sequence Sim.pm.2 977s Introducing 10 SNPs, 1/0 ref/read gaps, and 1 rearrangements 977s Finished SNPs 977s Finished ref gaps 977s Finished read gaps 977s Mutating sequence Sim.pm.1 977s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 977s Finished SNPs 977s Finished ref gaps 977s Finished read gaps 977s Mutated reference genome to subject genome 977s SNPs introduced: 17 977s Reference gaps introduced: 1 977s Read gaps introduced: 0 977s Rearrangements introduced: 1 977s Created read sampler 977s Sampling 97 reads 977s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 977s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 977s parsing sequence Sim.pm.1... 977s parsing sequence Sim.pm.2... 977s Parsed 110 reference bases 977s *** Run 64 of 100 977s /usr/bin/bowtie2 --rfg 44.3053745124288 --trim5 7 --score-min L,3.03662245353354,3.12063969962968 --np 14 -D 29 --local --rdg 26.0421028545027 -M 8 --large-index --cp-min 7 --cp-ival 1 -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 978s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 978s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '1' because it was < 2 characters long 978s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '11' because it was < 2 characters long 978s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '17' because it was < 2 characters long 978s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '26' because it was < 2 characters long 978s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '28' because it was < 2 characters long 978s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #2 of read '35' because it was < 2 characters long 978s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '36' because it was < 2 characters long 978s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '37' because it was < 2 characters long 978s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '38' because it was < 2 characters long 978s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 978s Warning: skipping read '42' because it was < 2 characters long 978s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 978s Warning: skipping read '45' because it was < 2 characters long 978s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '50' because it was < 2 characters long 978s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #2 of read '52' because it was < 2 characters long 978s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '53' because it was < 2 characters long 978s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '55' because it was < 2 characters long 978s Warning: skipping mate #2 of read '55' because it was < 2 characters long 978s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 978s Warning: skipping read '68' because it was < 2 characters long 978s Read 50 alignments... 978s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '76' because it was < 2 characters long 978s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '88' because it was < 2 characters long 978s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '89' because it was < 2 characters long 978s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '93' because it was < 2 characters long 978s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '94' because it was < 2 characters long 978s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '95' because it was < 2 characters long 978s Warning: skipping mate #1 of read '97' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '97' because it was < 2 characters long 978s Read 100 alignments... 978s 97 reads; of these: 978s 83 (85.57%) were paired; of these: 978s 83 (100.00%) aligned concordantly 0 times 978s 0 (0.00%) aligned concordantly exactly 1 time 978s 0 (0.00%) aligned concordantly >1 times 978s ---- 978s 83 pairs aligned concordantly 0 times; of these: 978s 0 (0.00%) aligned discordantly 1 time 978s ---- 978s 83 pairs aligned 0 times concordantly or discordantly; of these: 978s 166 mates make up the pairs; of these: 978s 166 (100.00%) aligned 0 times 978s 0 (0.00%) aligned exactly 1 time 978s 0 (0.00%) aligned >1 times 978s 14 (14.43%) were unpaired; of these: 978s 14 (100.00%) aligned 0 times 978s 0 (0.00%) aligned exactly 1 time 978s 0 (0.00%) aligned >1 times 978s 0.00% overall alignment rate 978s Read 150 alignments... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s 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line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s --- Summary --- 978s Read 1 reference strings 978s Checked 0 alignments, 0 edits 978s --------------- 978s PASSED 978s ALSO checking that bowtie2 and bowtie2-align match up 978s /usr/bin/bowtie2 --rfg 44.3053745124288 --trim5 7 --score-min L,3.03662245353354,3.12063969962968 --np 14 -D 29 --local --rdg 26.0421028545027 -M 8 --large-index --cp-min 7 --cp-ival 1 -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 978s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 978s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '1' because it was < 2 characters long 978s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '11' because it was < 2 characters long 978s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '17' because it was < 2 characters long 978s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '26' because it was < 2 characters long 978s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '28' because it was < 2 characters long 978s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #2 of read '35' because it was < 2 characters long 978s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '36' because it was < 2 characters long 978s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '37' because it was < 2 characters long 978s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '38' because it was < 2 characters long 978s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 978s Warning: skipping read '42' because it was < 2 characters long 978s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 978s Warning: skipping read '45' because it was < 2 characters long 978s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '50' because it was < 2 characters long 978s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #2 of read '52' because it was < 2 characters long 978s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '53' because it was < 2 characters long 978s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '55' because it was < 2 characters long 978s Warning: skipping mate #2 of read '55' because it was < 2 characters long 978s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 978s Warning: skipping read '68' because it was < 2 characters long 978s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '76' because it was < 2 characters long 978s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '88' because it was < 2 characters long 978s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '89' because it was < 2 characters long 978s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '93' because it was < 2 characters long 978s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '94' because it was < 2 characters long 978s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '95' because it was < 2 characters long 978s Warning: skipping mate #1 of read '97' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '97' because it was < 2 characters long 978s 97 reads; of these: 978s 83 (85.57%) were paired; of these: 978s 83 (100.00%) aligned concordantly 0 times 978s 0 (0.00%) aligned concordantly exactly 1 time 978s 0 (0.00%) aligned concordantly >1 times 978s ---- 978s 83 pairs aligned concordantly 0 times; of these: 978s 0 (0.00%) aligned discordantly 1 time 978s ---- 978s 83 pairs aligned 0 times concordantly or discordantly; of these: 978s 166 mates make up the pairs; of these: 978s 166 (100.00%) aligned 0 times 978s 0 (0.00%) aligned exactly 1 time 978s 0 (0.00%) aligned >1 times 978s 14 (14.43%) were unpaired; of these: 978s 14 (100.00%) aligned 0 times 978s 0 (0.00%) aligned exactly 1 time 978s 0 (0.00%) aligned >1 times 978s 0.00% overall alignment rate 978s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 978s Flattened IUPAC characters 978s Mutating sequence Sim.pm.1 978s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 978s Finished SNPs 978s Finished ref gaps 978s Finished read gaps 978s Mutating sequence Sim.pm.2 978s Introducing 18 SNPs, 1/0 ref/read gaps, and 0 rearrangements 978s Finished SNPs 978s Finished ref gaps 978s Finished read gaps 978s Mutated reference genome to subject genome 978s SNPs introduced: 23 978s Reference gaps introduced: 1 978s Read gaps introduced: 0 978s Rearrangements introduced: 0 978s Created read sampler 978s Sampling 109 reads 978s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 978s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 978s parsing sequence Sim.pm.1... 978s parsing sequence Sim.pm.2... 978s Parsed 110 reference bases 978s *** Run 65 of 100 978s /usr/bin/bowtie2 --score-min L,4.18431731903319,1.19726397505376 --large-index --rfg 24.5966082418858 --mp 9.09718786005907,6.25138023931874 --trim3 8 --cp-ival 2 --mm --np 2 --cp-min 3 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 978s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '3' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 978s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '4' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 978s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '5' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 978s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '6' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 978s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '12' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 978s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '15' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 978s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 978s Warning: skipping read '23' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 978s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 978s Warning: skipping read '37' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 978s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 978s Warning: skipping read '38' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 978s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '40' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 978s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '48' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 978s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '51' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 978s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #2 of read '63' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 978s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '65' because it was < 2 characters long 978s Read 50 alignments... 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 978s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '67' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 978s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '68' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 978s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '69' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 978s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '76' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 978s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '82' because it was < 2 characters long 978s Read 100 alignments... 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 978s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 978s Warning: skipping mate #1 of read '85' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 978s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #2 of read '86' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 978s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #2 of read '99' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 978s Warning: skipping mate #2 of read '104' because length (1) <= # seed mismatches (0) 978s Warning: skipping mate #2 of read '104' because it was < 2 characters long 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 978s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 978s 109 reads; of these: 978s 90 (82.57%) were paired; of these: 978s 90 (100.00%) aligned concordantly 0 times 978s 0 (0.00%) aligned concordantly exactly 1 time 978s 0 (0.00%) aligned concordantly >1 times 978s ---- 978s 90 pairs aligned concordantly 0 times; of these: 978s 0 (0.00%) aligned discordantly 1 time 978s ---- 978s 90 pairs aligned 0 times concordantly or discordantly; of these: 978s 180 mates make up the pairs; of these: 978s 157 (87.22%) aligned 0 times 978s 12 (6.67%) aligned exactly 1 time 978s 11 (6.11%) aligned >1 times 978s 19 (17.43%) were unpaired; of these: 978s 17 (89.47%) aligned 0 times 978s 2 (10.53%) aligned exactly 1 time 978s 0 (0.00%) aligned >1 times 978s 12.56% overall alignment rate 978s Read 150 alignments... 978s Read 200 alignments... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s GGG 978s GGG 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s CGA 978s CGA 978s Processing line... 978s Processing line... 978s ATAGTGCGACCGCGTC 978s ATAGTGCGACCGCGTC 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s GCGGAA 978s GCGGAA 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s CACAGC 978s CACAGC 978s Processing line... 978s Processing line... 978s CAGCAT 978s CAGCAT 978s Processing line... 978s Processing line... 978s AAGGGCCT 978s AAGGGCCT 978s Processing line... 978s Processing line... 978s GGGA 978s GGGA 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s GAATGCAGATGGGAC 978s GAATGCAGATGGGAC 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s GATGGGACAGGGGAG 978s GATGGGACAGGGGAG 978s Processing line... 978s Processing line... 978s GAT 978s GAT 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s TCCA 978s TCCA 978s Processing line... 978s Processing line... 978s GGGACAGG 978s GGGACAGG 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s GGG 978s GGG 978s /usr/bin/bowtie2 --score-min L,4.18431731903319,1.19726397505376 --large-index --rfg 24.5966082418858 --mp 9.09718786005907,6.25138023931874 --trim3 8 --cp-ival 2 --mm --np 2 --cp-min 3 -f -p 4 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s GCAT 978s GCAT 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s CA 978s CA 978s Processing line... 978s Processing line... 978s AGA 978s AGA 978s Processing line... 978s Processing line... 978s TCC 978s TCC 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s GG 978s GG 978s Processing line... 978s Processing line... 978s AG 978s AG 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s AGCATAG 978s AGCATAG 978s Processing line... 978s Processing line... 978s AGGGCCTC 978s AGGGCCTC 978s Processing line... 978s CGAC 978s CGAC 978s Processing line... 978s Processing line... 978s GGGAG 978s GGGAG 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s GA 978s GA 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s Processing line... 978s --- Summary --- 978s Read 1 reference strings 978s Checked 25 alignments, 0 edits 978s --------------- 978s PASSED 978s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 979s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '3' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 979s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '4' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 979s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '5' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 979s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '6' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 979s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '12' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 979s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '15' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 979s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 979s Warning: skipping read '23' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 979s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '65' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 979s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '67' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 979s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '68' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 979s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '69' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 979s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '76' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 979s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '51' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 979s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 979s Warning: skipping read '37' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 979s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 979s Warning: skipping read '38' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 979s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '40' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 979s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '82' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 979s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '85' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 979s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 979s Warning: skipping mate #2 of read '86' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 979s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '48' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 979s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 979s Warning: skipping mate #2 of read '63' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 979s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 979s Warning: skipping mate #2 of read '99' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 979s Warning: skipping mate #2 of read '104' because length (1) <= # seed mismatches (0) 979s Warning: skipping mate #2 of read '104' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 979s 109 reads; of these: 979s 90 (82.57%) were paired; of these: 979s 90 (100.00%) aligned concordantly 0 times 979s 0 (0.00%) aligned concordantly exactly 1 time 979s 0 (0.00%) aligned concordantly >1 times 979s ---- 979s 90 pairs aligned concordantly 0 times; of these: 979s 0 (0.00%) aligned discordantly 1 time 979s ---- 979s 90 pairs aligned 0 times concordantly or discordantly; of these: 979s 180 mates make up the pairs; of these: 979s 157 (87.22%) aligned 0 times 979s 12 (6.67%) aligned exactly 1 time 979s 11 (6.11%) aligned >1 times 979s 19 (17.43%) were unpaired; of these: 979s 17 (89.47%) aligned 0 times 979s 2 (10.53%) aligned exactly 1 time 979s 0 (0.00%) aligned >1 times 979s 12.56% overall alignment rate 979s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 979s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 979s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 979s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 979s /usr/bin/bowtie2 --score-min L,4.18431731903319,1.19726397505376 --large-index --rfg 24.5966082418858 --mp 9.09718786005907,6.25138023931874 --trim3 8 --cp-ival 2 --mm --np 2 --cp-min 3 -f -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 979s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '3' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 979s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 979s Warning: skipping read '23' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 979s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '4' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 979s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '5' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 979s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '6' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 979s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '12' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 979s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '15' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 979s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '65' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 979s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '51' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 979s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '67' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 979s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 979s Warning: skipping mate #2 of read '63' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 979s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '82' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 979s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '85' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 979s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 979s Warning: skipping mate #2 of read '86' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 979s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '68' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 979s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '69' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 979s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '76' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 979s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 979s Warning: skipping read '37' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 979s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 979s Warning: skipping read '38' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 979s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '40' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 979s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 979s Warning: skipping mate #1 of read '48' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 979s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 979s Warning: skipping mate #2 of read '99' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 979s Warning: skipping mate #2 of read '104' because length (1) <= # seed mismatches (0) 979s Warning: skipping mate #2 of read '104' because it was < 2 characters long 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 979s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 979s 109 reads; of these: 979s 90 (82.57%) were paired; of these: 979s 90 (100.00%) aligned concordantly 0 times 979s 0 (0.00%) aligned concordantly exactly 1 time 979s 0 (0.00%) aligned concordantly >1 times 979s ---- 979s 90 pairs aligned concordantly 0 times; of these: 979s 0 (0.00%) aligned discordantly 1 time 979s ---- 979s 90 pairs aligned 0 times concordantly or discordantly; of these: 979s 180 mates make up the pairs; of these: 979s 157 (87.22%) aligned 0 times 979s 12 (6.67%) aligned exactly 1 time 979s 11 (6.11%) aligned >1 times 979s 19 (17.43%) were unpaired; of these: 979s 17 (89.47%) aligned 0 times 979s 2 (10.53%) aligned exactly 1 time 979s 0 (0.00%) aligned >1 times 979s 12.56% overall alignment rate 979s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 979s Flattened IUPAC characters 979s Mutating sequence Sim.pm.2 979s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 979s Finished SNPs 979s Finished ref gaps 979s Finished read gaps 979s Mutating sequence Sim.pm.1 979s Introducing 9 SNPs, 0/1 ref/read gaps, and 1 rearrangements 979s Finished SNPs 979s Finished ref gaps 979s Finished read gaps 979s Mutated reference genome to subject genome 979s SNPs introduced: 11 979s Reference gaps introduced: 0 979s Read gaps introduced: 1 979s Rearrangements introduced: 1 979s Created read sampler 979s Sampling 88 reads 979s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 979s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 979s parsing sequence Sim.pm.1... 979s parsing sequence Sim.pm.2... 979s Parsed 110 reference bases 979s *** Run 66 of 100 979s /usr/bin/bowtie2 --rdg 38.3629147796183 --rfg 47.6379775699359,5.92198236443498 --large-index --score-min L,2.21655491013414,5.63783333507173 --cp-min 9 --np 5 --cp-ival 5 -D 14 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 979s 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 979s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 979s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 979s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s 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 979s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 979s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 979s 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 979s 88 reads; of these: 979s 88 (100.00%) were unpaired; of these: 979s 64 (72.73%) aligned 0 times 979s 21 (23.86%) aligned exactly 1 time 979s 3 (3.41%) aligned >1 times 979s 27.27% overall alignment rate 979s Read 50 alignments... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s GGGAG 979s GGGAG 979s Processing line... 979s ATGGG 979s ATGGG 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s GGGGAGGCGAACAAAGGGCCTCGC 979s GGGGAGGCGAACAAAGGGCCTCGC 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s TCGCAGCGGAA 979s TCGCAGCGGAA 979s Processing line... 979s GAACAAAGGGCCT 979s GAACAAAGGGCCT 979s Processing line... 979s Processing line... 979s AGGGCCTCGCAGCGG 979s AGGGCCTCGCAGCGG 979s Processing line... 979s Processing line... 979s Processing line... 979s CAGATGGGACAGGG 979s CAGATGGGACAGGG 979s Processing line... 979s Processing line... 979s GGCGAACAAAG 979s GGCGAACAAAG 979s Processing line... 979s Processing line... 979s ACAGCATAGTGCGACCGCGT 979s ACAGCATAGTGCGACCGCGT 979s Processing line... 979s GGGCCTC 979s GGGCCTC 979s Processing line... 979s ACAGGGG 979s ACAGGGG 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s CA 979s CA 979s Processing line... 979s Processing line... 979s ATGGG 979s ATGGG 979s Processing line... 979s Processing line... 979s Processing line... 979s ACAGCATAGTGCGACCGCGT 979s ACAGCATAGTGCGACCGCGT 979s Processing line... 979s Processing line... 979s GGCCTCGCAG 979s GGCCTCGCAG 979s Processing line... 979s GGGCCTCGCAGCGGAAGC 979s GGGCCTCGCAGCGGAAGC 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s ATGGGA 979s ATGGGA 979s Processing line... 979s Processing line... 979s Processing line... 979s ACC 979s ACC 979s Processing line... 979s GGC 979s GGC 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s AACAAAGGGCCT 979s AACAAAGGGCCT 979s Processing line... 979s /usr/bin/bowtie2 --rdg 38.3629147796183 --rfg 47.6379775699359,5.92198236443498 --large-index --score-min L,2.21655491013414,5.63783333507173 --cp-min 9 --np 5 --cp-ival 5 -D 14 --qseq -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 979s GG 979s GG 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s GAATGCAGATGGGACAGGGGAGGCGAACAAAG 979s GAATGCAGATGGGACAGGGGAGGCGAACAAAG 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s Processing line... 979s ACAGGGGAG 979s ACAGGGGAG 979s Processing line... 979s Processing line... 979s AAGC 979s AAGC 979s --- Summary --- 979s Read 1 reference strings 979s Checked 24 alignments, 0 edits 979s --------------- 979s PASSED 979s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 980s 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 980s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 980s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 980s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 980s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 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 980s 88 reads; of these: 980s 88 (100.00%) were unpaired; of these: 980s 64 (72.73%) aligned 0 times 980s 21 (23.86%) aligned exactly 1 time 980s 3 (3.41%) aligned >1 times 980s 27.27% overall alignment rate 980s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 980s Flattened IUPAC characters 980s Mutating sequence Sim.pm.1 980s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 980s Finished SNPs 980s Finished ref gaps 980s Finished read gaps 980s Mutating sequence Sim.pm.2 980s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 980s Finished SNPs 980s Finished ref gaps 980s Finished read gaps 980s Mutated reference genome to subject genome 980s SNPs introduced: 9 980s Reference gaps introduced: 0 980s Read gaps introduced: 0 980s Rearrangements introduced: 0 980s Created read sampler 980s Sampling 100 reads 980s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 980s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 980s *** Run 67 of 100 980s /usr/bin/bowtie2 --score-min L,2.28948810305749,6.47987494794157 --gbar 4 --n-ceil 0.902019003718912,0.405992944729235 --trim5 1 --np 6 --norc -k 13 --large-index --local --trim3 8 --rdg 11.5190852475922 --cp-ival 1 --cp-min 5 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 980s parsing sequence Sim.pm.1... 980s parsing sequence Sim.pm.2... 980s Parsed 110 reference bases 980s Warning: skipping read '0' because length (1) <= # seed mismatches (0) 980s Warning: skipping read '0' because it was < 2 characters long 980s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '4' because it was < 2 characters long 980s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 980s Warning: skipping read '9' because it was < 2 characters long 980s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '15' because it was < 2 characters long 980s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '19' because it was < 2 characters long 980s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '20' because it was < 2 characters long 980s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '22' because it was < 2 characters long 980s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '23' because it was < 2 characters long 980s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '28' because it was < 2 characters long 980s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '31' because it was < 2 characters long 980s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '34' because it was < 2 characters long 980s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '35' because it was < 2 characters long 980s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '39' because it was < 2 characters long 980s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '40' because it was < 2 characters long 980s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '42' because it was < 2 characters long 980s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '44' because it was < 2 characters long 980s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 980s Warning: skipping read '48' because it was < 2 characters long 980s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '51' because it was < 2 characters long 980s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '52' because it was < 2 characters long 980s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '62' because it was < 2 characters long 980s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '63' because it was < 2 characters long 980s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '64' because it was < 2 characters long 980s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '65' because it was < 2 characters long 980s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '76' because it was < 2 characters long 980s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '77' because it was < 2 characters long 980s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '86' because it was < 2 characters long 980s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '89' because it was < 2 characters long 980s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '92' because it was < 2 characters long 980s Warning: skipping read '98' because length (1) <= # seed mismatches (0) 980s Warning: skipping read '98' because it was < 2 characters long 980s 100 reads; of these: 980s 100 (100.00%) were unpaired; of these: 980s 100 (100.00%) aligned 0 times 980s 0 (0.00%) aligned exactly 1 time 980s 0 (0.00%) aligned >1 times 980s 0.00% overall alignment rate 980s Read 50 alignments... 980s Read 100 alignments... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s Processing line... 980s --- Summary --- 980s Read 1 reference strings 980s Checked 0 alignments, 0 edits 980s --------------- 980s PASSED 980s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 980s /usr/bin/bowtie2 --score-min L,2.28948810305749,6.47987494794157 --gbar 4 --n-ceil 0.902019003718912,0.405992944729235 --trim5 1 --np 6 --norc -k 13 --large-index --local --trim3 8 --rdg 11.5190852475922 --cp-ival 1 --cp-min 5 -r -p 3 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 980s Warning: skipping read '0' because length (1) <= # seed mismatches (0) 980s Warning: skipping read '0' because it was < 2 characters long 980s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '4' because it was < 2 characters long 980s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 980s Warning: skipping read '9' because it was < 2 characters long 980s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '15' because it was < 2 characters long 980s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '19' because it was < 2 characters long 980s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '20' because it was < 2 characters long 980s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '22' because it was < 2 characters long 980s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '23' because it was < 2 characters long 980s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '28' because it was < 2 characters long 980s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '31' because it was < 2 characters long 980s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '34' because it was < 2 characters long 980s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '35' because it was < 2 characters long 980s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '39' because it was < 2 characters long 980s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '40' because it was < 2 characters long 980s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '42' because it was < 2 characters long 980s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '44' because it was < 2 characters long 980s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '64' because it was < 2 characters long 980s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '65' because it was < 2 characters long 980s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '76' because it was < 2 characters long 980s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '77' because it was < 2 characters long 980s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 980s Warning: skipping read '48' because it was < 2 characters long 980s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '51' because it was < 2 characters long 980s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '52' because it was < 2 characters long 980s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '62' because it was < 2 characters long 980s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '63' because it was < 2 characters long 980s Warning: skipping read '98' because length (1) <= # seed mismatches (0) 980s Warning: skipping read '98' because it was < 2 characters long 980s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '86' because it was < 2 characters long 980s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '89' because it was < 2 characters long 980s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 980s Warning: skipping read '92' because it was < 2 characters long 980s 100 reads; of these: 980s 100 (100.00%) were unpaired; of these: 980s 100 (100.00%) aligned 0 times 980s 0 (0.00%) aligned exactly 1 time 980s 0 (0.00%) aligned >1 times 980s 0.00% overall alignment rate 980s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 980s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 980s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 980s Flattened IUPAC characters 980s Mutating sequence Sim.pm.2 980s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 980s Finished SNPs 980s Finished ref gaps 980s Finished read gaps 980s Mutating sequence Sim.pm.1 980s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 980s Finished SNPs 980s Finished ref gaps 980s Finished read gaps 980s Mutated reference genome to subject genome 980s SNPs introduced: 9 980s Reference gaps introduced: 1 980s Read gaps introduced: 1 980s Rearrangements introduced: 0 980s Created read sampler 980s Sampling 141 reads 980s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 980s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 980s parsing sequence Sim.pm.1... 980s parsing sequence Sim.pm.2... 980s Parsed 110 reference bases 980s *** Run 68 of 100 980s /usr/bin/bowtie2 --mp 7.72600061852022,6.5343647261248 --rdg 14.0902554707936,17.5641102217833 --trim5 2 --rfg 28.1796188001836 --local --large-index -k 6 --score-min L,9.92007616963539,5.16078394403059 --cp-min 2 --np 2 --nofw --cp-ival 3 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 981s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '5' because it was < 2 characters long 981s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 981s Warning: skipping read '12' because it was < 2 characters long 981s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '14' because it was < 2 characters long 981s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '15' because it was < 2 characters long 981s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '27' because it was < 2 characters long 981s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '45' because it was < 2 characters long 981s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '49' because it was < 2 characters long 981s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '57' because it was < 2 characters long 981s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 981s Warning: skipping read '70' because it was < 2 characters long 981s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 981s Warning: skipping read '76' because it was < 2 characters long 981s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '78' because it was < 2 characters long 981s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '98' because it was < 2 characters long 981s Warning: skipping read '121' because length (1) <= # seed mismatches (0) 981s Warning: skipping read '121' because it was < 2 characters long 981s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '136' because it was < 2 characters long 981s 141 reads; of these: 981s 141 (100.00%) were unpaired; of these: 981s 141 (100.00%) aligned 0 times 981s 0 (0.00%) aligned exactly 1 time 981s 0 (0.00%) aligned >1 times 981s 0.00% overall alignment rate 981s Read 50 alignments... 981s Read 100 alignments... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s --- Summary --- 981s Read 1 reference strings 981s Checked 0 alignments, 0 edits 981s --------------- 981s PASSED 981s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 981s /usr/bin/bowtie2 --mp 7.72600061852022,6.5343647261248 --rdg 14.0902554707936,17.5641102217833 --trim5 2 --rfg 28.1796188001836 --local --large-index -k 6 --score-min L,9.92007616963539,5.16078394403059 --cp-min 2 --np 2 --nofw --cp-ival 3 -q -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 981s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '5' because it was < 2 characters long 981s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 981s Warning: skipping read '12' because it was < 2 characters long 981s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '14' because it was < 2 characters long 981s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '15' because it was < 2 characters long 981s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '27' because it was < 2 characters long 981s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '45' because it was < 2 characters long 981s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '49' because it was < 2 characters long 981s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '57' because it was < 2 characters long 981s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '98' because it was < 2 characters long 981s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 981s Warning: skipping read '70' because it was < 2 characters long 981s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 981s Warning: skipping read '76' because it was < 2 characters long 981s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '78' because it was < 2 characters long 981s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 981s Warning: skipping read '136' because it was < 2 characters long 981s Warning: skipping read '121' because length (1) <= # seed mismatches (0) 981s Warning: skipping read '121' because it was < 2 characters long 981s 141 reads; of these: 981s 141 (100.00%) were unpaired; of these: 981s 141 (100.00%) aligned 0 times 981s 0 (0.00%) aligned exactly 1 time 981s 0 (0.00%) aligned >1 times 981s 0.00% overall alignment rate 981s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 981s Flattened IUPAC characters 981s Mutating sequence Sim.pm.2 981s Introducing 16 SNPs, 2/2 ref/read gaps, and 0 rearrangements 981s Finished SNPs 981s Finished ref gaps 981s Finished read gaps 981s Mutating sequence Sim.pm.1 981s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 981s Finished SNPs 981s Finished ref gaps 981s Finished read gaps 981s Mutated reference genome to subject genome 981s SNPs introduced: 21 981s Reference gaps introduced: 2 981s Read gaps introduced: 2 981s Rearrangements introduced: 0 981s Created read sampler 981s Sampling 59 reads 981s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 981s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 981s parsing sequence Sim.pm.1... 981s parsing sequence Sim.pm.2... 981s Parsed 110 reference bases 981s *** Run 69 of 100 981s /usr/bin/bowtie2 --large-index --trim3 8 --rdg 42.4312931623589 --local --cp-ival 1 --mm --cp-min 4 --n-ceil 1.47185483370333,0.203737403646894 --score-min L,8.97398122110796,6.92985086610416 -R 2 --np 7 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 981s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 981s 59 reads; of these: 981s 59 (100.00%) were unpaired; of these: 981s 59 (100.00%) aligned 0 times 981s 0 (0.00%) aligned exactly 1 time 981s 0 (0.00%) aligned >1 times 981s 0.00% overall alignment rate 981s Read 50 alignments... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s Processing line... 981s --- Summary --- 981s Read 1 reference strings 981s Checked 0 alignments, 0 edits 981s --------------- 981s /usr/bin/bowtie2 --large-index --trim3 8 --rdg 42.4312931623589 --local --cp-ival 1 --mm --cp-min 4 --n-ceil 1.47185483370333,0.203737403646894 --score-min L,8.97398122110796,6.92985086610416 -R 2 --np 7 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 981s PASSED 981s ALSO checking that bowtie2 and bowtie2-align match up 981s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 981s 59 reads; of these: 981s 59 (100.00%) were unpaired; of these: 981s 59 (100.00%) aligned 0 times 981s 0 (0.00%) aligned exactly 1 time 981s 0 (0.00%) aligned >1 times 981s 0.00% overall alignment rate 981s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 981s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 981s /usr/bin/bowtie2 --large-index --trim3 8 --rdg 42.4312931623589 --local --cp-ival 1 --mm --cp-min 4 --n-ceil 1.47185483370333,0.203737403646894 --score-min L,8.97398122110796,6.92985086610416 -R 2 --np 7 --qseq -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 981s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 981s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 981s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 981s 59 reads; of these: 981s 59 (100.00%) were unpaired; of these: 981s 59 (100.00%) aligned 0 times 981s 0 (0.00%) aligned exactly 1 time 981s 0 (0.00%) aligned >1 times 981s 0.00% overall alignment rate 981s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 981s Flattened IUPAC characters 981s Mutating sequence Sim.pm.2 981s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 981s Finished SNPs 981s Finished ref gaps 981s Finished read gaps 981s Mutating sequence Sim.pm.1 981s Introducing 4 SNPs, 1/1 ref/read gaps, and 2 rearrangements 981s Finished SNPs 981s Finished ref gaps 981s Finished read gaps 981s Mutated reference genome to subject genome 981s SNPs introduced: 7 981s Reference gaps introduced: 2 981s Read gaps introduced: 1 981s Rearrangements introduced: 3 981s Created read sampler 981s Sampling 72 reads 981s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 981s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 981s parsing sequence Sim.pm.1... 981s parsing sequence Sim.pm.2... 981s Parsed 110 reference bases 981s *** Run 70 of 100 981s /usr/bin/bowtie2 -R 1 --nofw --score-min L,5.31451776052546,1.85792810699152 --gbar 2 --trim5 8 --cp-ival 2 --mm --cp-min 4 --large-index -a --mp 9.55216702862373,7.11549258596118 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 982s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 982s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '2' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 982s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '11' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 982s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '15' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 982s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '17' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 982s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '19' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 982s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '21' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 982s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '23' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 982s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '24' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 982s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '27' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 982s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 982s Warning: skipping read '29' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 982s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '34' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 982s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '36' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 982s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '44' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 982s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '47' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 982s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '50' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 982s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '51' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 982s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '52' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 982s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '54' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 982s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '56' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 982s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '57' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 982s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '60' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 982s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '64' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 982s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 982s Warning: skipping read '65' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 982s 72 reads; of these: 982s 72 (100.00%) were unpaired; of these: 982s 65 (90.28%) aligned 0 times 982s 4 (5.56%) aligned exactly 1 time 982s 3 (4.17%) aligned >1 times 982s 9.72% overall alignment rate 982s Read 50 alignments... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s TCG 982s TCG 982s Processing line... 982s TCG 982s TCG 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s CGCATGT 982s CGCATGT 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s ACC 982s ACC 982s Processing line... 982s Processing line... 982s Processing line... 982s CAGG 982s CAGG 982s Processing line... 982s CAGG 982s CAGG 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s TG 982s TG 982s Processing line... 982s TG 982s TG 982s Processing line... 982s TG 982s TG 982s Processing line... 982s TG 982s TG 982s Processing line... 982s Processing line... 982s Processing line... 982s CAGGGGA 982s CAGGGGA 982s Processing line... 982s Processing line... 982s Processing line... 982s GGACGC 982s GGACGC 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s --- Summary --- 982s Read 1 reference strings 982s /usr/bin/bowtie2 -R 1 --nofw --score-min L,5.31451776052546,1.85792810699152 --gbar 2 --trim5 8 --cp-ival 2 --mm --cp-min 4 --large-index -a --mp 9.55216702862373,7.11549258596118 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 982s Checked 12 alignments, 0 edits 982s --------------- 982s PASSED 982s ALSO checking that bowtie2 and bowtie2-align match up 982s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 982s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '2' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 982s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '11' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 982s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '15' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 982s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '17' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 982s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '19' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 982s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '21' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 982s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '23' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 982s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '24' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 982s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '27' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 982s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 982s Warning: skipping read '29' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 982s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '34' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 982s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '36' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 982s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '44' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 982s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '47' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 982s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '50' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 982s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '51' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 982s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '52' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 982s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '54' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 982s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '56' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 982s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '57' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 982s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '60' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 982s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '64' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 982s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 982s Warning: skipping read '65' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 982s 72 reads; of these: 982s 72 (100.00%) were unpaired; of these: 982s 65 (90.28%) aligned 0 times 982s 4 (5.56%) aligned exactly 1 time 982s 3 (4.17%) aligned >1 times 982s 9.72% overall alignment rate 982s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 982s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 982s /usr/bin/bowtie2 -R 1 --nofw --score-min L,5.31451776052546,1.85792810699152 --gbar 2 --trim5 8 --cp-ival 2 --mm --cp-min 4 --large-index -a --mp 9.55216702862373,7.11549258596118 -r -p 2 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 982s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 982s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '2' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 982s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '11' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 982s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '15' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 982s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '17' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 982s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '19' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 982s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '21' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 982s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '23' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 982s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '24' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 982s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '27' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 982s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 982s Warning: skipping read '29' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 982s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '34' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 982s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '36' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 982s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '50' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 982s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '51' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 982s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '52' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 982s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '54' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 982s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '56' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 982s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '57' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 982s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '60' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 982s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '44' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 982s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '64' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 982s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 982s Warning: skipping read '65' because it was < 2 characters long 982s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 982s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 982s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 982s Warning: skipping read '47' because it was < 2 characters long 982s 72 reads; of these: 982s 72 (100.00%) were unpaired; of these: 982s 65 (90.28%) aligned 0 times 982s 4 (5.56%) aligned exactly 1 time 982s 3 (4.17%) aligned >1 times 982s 9.72% overall alignment rate 982s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 982s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 982s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 982s Flattened IUPAC characters 982s Mutating sequence Sim.pm.1 982s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 982s Finished SNPs 982s Finished ref gaps 982s Finished read gaps 982s Mutating sequence Sim.pm.2 982s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 982s Finished SNPs 982s Finished ref gaps 982s Finished read gaps 982s Mutated reference genome to subject genome 982s SNPs introduced: 8 982s Reference gaps introduced: 0 982s Read gaps introduced: 0 982s Rearrangements introduced: 2 982s Created read sampler 982s Sampling 41 reads 982s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 982s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 982s parsing sequence Sim.pm.1... 982s parsing sequence Sim.pm.2... 982s Parsed 110 reference bases 982s *** Run 71 of 100 982s /usr/bin/bowtie2 --np 6 --score-min L,4.62332824896225,4.79639833313127 --gbar 1 --trim5 5 --rfg 6.64298002778241 --cp-ival 2 --cp-min 3 --ma 31.6811139969596 --large-index --mp 5.94760361944619,1.78193350344167 --trim3 5 --rdg 47.3147669661582 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 982s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 982s 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 982s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 982s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 982s 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 982s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 982s 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 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 982s 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 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 982s 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 982s 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 982s 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 982s 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 982s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (0) 982s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 982s 41 reads; of these: 982s 33 (80.49%) were paired; of these: 982s 33 (100.00%) aligned concordantly 0 times 982s 0 (0.00%) aligned concordantly exactly 1 time 982s 0 (0.00%) aligned concordantly >1 times 982s ---- 982s 33 pairs aligned concordantly 0 times; of these: 982s 1 (3.03%) aligned discordantly 1 time 982s ---- 982s 32 pairs aligned 0 times concordantly or discordantly; of these: 982s 64 mates make up the pairs; of these: 982s 60 (93.75%) aligned 0 times 982s 4 (6.25%) aligned exactly 1 time 982s 0 (0.00%) aligned >1 times 982s 8 (19.51%) were unpaired; of these: 982s 8 (100.00%) aligned 0 times 982s 0 (0.00%) aligned exactly 1 time 982s 0 (0.00%) aligned >1 times 982s 8.11% overall alignment rate 982s Read 50 alignments... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s GGGAGGCGAACAAAGGGCCTCGCAG 982s GGGAGGCGAACAAAGGGCCTCGCAG 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s GGCGAACA 982s GGCGAACA 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s GAAGC 982s GAAGC 982s Processing line... 982s GATGGGACAGGGGAGGCGA 982s GATGGGACAGGGGAGGCGA 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s GACGCACAGCATAGTGC 982s GACGCACAGCATAGTGC 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s ACAGGGGAGGCG 982s ACAGGGGAGGCG 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s Processing line... 982s --- Summary --- 982s Read 1 reference strings 982s Checked 6 alignments, 0 edits 982s --------------- 982s PASSED 982s Flattened IUPAC characters 982s Mutating sequence Sim.pm.2 982s Introducing 12 SNPs, 0/1 ref/read gaps, and 3 rearrangements 982s Finished SNPs 982s Finished ref gaps 982s Finished read gaps 982s *** Run 72 of 100 982s /usr/bin/bowtie2 --large-index -k 13 --mp 2.83231225644543,2.49151020812726 --rdg 6.45826851062143,2.96269183318541 --local --cp-ival 1 --cp-min 3 --score-min L,1.21601627551084,2.67087756191594 --gbar 1 -N 0 -R 4 -r -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.raw -2 /tmp/Sim.pm.5TNUEKCv_2.raw 982s Mutating sequence Sim.pm.1 982s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 982s Finished SNPs 982s Finished ref gaps 982s Finished read gaps 982s Mutated reference genome to subject genome 982s SNPs introduced: 13 982s Reference gaps introduced: 0 982s Read gaps introduced: 1 982s Rearrangements introduced: 3 982s Created read sampler 982s Sampling 64 reads 982s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 982s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 982s parsing sequence Sim.pm.1... 982s parsing sequence Sim.pm.2... 982s Parsed 110 reference bases 983s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 983s Warning: skipping mate #1 of read '14' because it was < 2 characters long 983s Read 50 alignments... 983s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 983s Warning: skipping mate #2 of read '53' because it was < 2 characters long 983s 64 reads; of these: 983s 64 (100.00%) were paired; of these: 983s 64 (100.00%) aligned concordantly 0 times 983s 0 (0.00%) aligned concordantly exactly 1 time 983s 0 (0.00%) aligned concordantly >1 times 983s ---- 983s 64 pairs aligned concordantly 0 times; of these: 983s 0 (0.00%) aligned discordantly 1 time 983s ---- 983s 64 pairs aligned 0 times concordantly or discordantly; of these: 983s 128 mates make up the pairs; of these: 983s 128 (100.00%) aligned 0 times 983s 0 (0.00%) aligned exactly 1 time 983s 0 (0.00%) aligned >1 times 983s 0.00% overall alignment rate 983s Read 100 alignments... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s --- Summary --- 983s Read 1 reference strings 983s Checked 0 alignments, 0 edits 983s --------------- 983s PASSED 983s Flattened IUPAC characters 983s Mutating sequence Sim.pm.1 983s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 983s Finished SNPs 983s Finished ref gaps 983s Finished read gaps 983s Mutating sequence Sim.pm.2 983s Introducing 10 SNPs, 2/0 ref/read gaps, and 0 rearrangements 983s Finished SNPs 983s Finished ref gaps 983s Finished read gaps 983s Mutated reference genome to subject genome 983s SNPs introduced: 18 983s Reference gaps introduced: 3 983s Read gaps introduced: 0 983s Rearrangements introduced: 0 983s Created read sampler 983s Sampling 38 reads 983s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 983s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 983s parsing sequence Sim.pm.1... 983s parsing sequence Sim.pm.2... 983s *** Run 73 of 100 983s /usr/bin/bowtie2 --trim5 4 --rfg 24.4231752077909 --score-min L,5.07840776148469,2.58432295856413 -D 13 --rdg 27.309523144881,2.10866486478435 --mp 7.69214785789725,4.44258588581337 -a --local --large-index --cp-min 4 --mm --cp-ival 1 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 983s Parsed 110 reference bases 983s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '1' because it was < 2 characters long 983s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '5' because it was < 2 characters long 983s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '15' because it was < 2 characters long 983s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 983s Warning: skipping read '17' because it was < 2 characters long 983s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '19' because it was < 2 characters long 983s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '28' because it was < 2 characters long 983s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '36' because it was < 2 characters long 983s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '37' because it was < 2 characters long 983s 38 reads; of these: 983s 38 (100.00%) were unpaired; of these: 983s 38 (100.00%) aligned 0 times 983s 0 (0.00%) aligned exactly 1 time 983s 0 (0.00%) aligned >1 times 983s 0.00% overall alignment rate 983s Processing line... 983s Processing line... 983s /usr/bin/bowtie2 --trim5 4 --rfg 24.4231752077909 --score-min L,5.07840776148469,2.58432295856413 -D 13 --rdg 27.309523144881,2.10866486478435 --mp 7.69214785789725,4.44258588581337 -a --local --large-index --cp-min 4 --mm --cp-ival 1 -q -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s --- Summary --- 983s Read 1 reference strings 983s Checked 0 alignments, 0 edits 983s --------------- 983s PASSED 983s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 983s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '1' because it was < 2 characters long 983s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '5' because it was < 2 characters long 983s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '15' because it was < 2 characters long 983s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 983s Warning: skipping read '17' because it was < 2 characters long 983s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '19' because it was < 2 characters long 983s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '28' because it was < 2 characters long 983s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '36' because it was < 2 characters long 983s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '37' because it was < 2 characters long 983s 38 reads; of these: 983s 38 (100.00%) were unpaired; of these: 983s 38 (100.00%) aligned 0 times 983s 0 (0.00%) aligned exactly 1 time 983s 0 (0.00%) aligned >1 times 983s 0.00% overall alignment rate 983s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 983s Flattened IUPAC characters 983s Mutating sequence Sim.pm.2 983s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 983s Finished SNPs 983s Finished ref gaps 983s Finished read gaps 983s Mutating sequence Sim.pm.1 983s Introducing 11 SNPs, 0/1 ref/read gaps, and 2 rearrangements 983s Finished SNPs 983s Finished ref gaps 983s Finished read gaps 983s Mutated reference genome to subject genome 983s SNPs introduced: 17 983s Reference gaps introduced: 0 983s Read gaps introduced: 2 983s Rearrangements introduced: 3 983s Created read sampler 983s Sampling 145 reads 983s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 983s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 983s parsing sequence Sim.pm.1... 983s parsing sequence Sim.pm.2... 983s Parsed 110 reference bases 983s *** Run 74 of 100 983s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --mm --local --mp 1.55405814624156,1.54786211744336 -a --rdg 26.0889845651405,14.7637838697627 --large-index -R 1 --rfg 17.7374127109908,10.9475605024689 --trim5 4 --score-min L,4.30455823097725,2.27795022429236 --n-ceil 0.705801269036302,0.85839408145449 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 983s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '16' because it was < 2 characters long 983s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 983s Warning: skipping read '26' because it was < 2 characters long 983s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '32' because it was < 2 characters long 983s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '41' because it was < 2 characters long 983s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '48' because it was < 2 characters long 983s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '63' because it was < 2 characters long 983s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '66' because it was < 2 characters long 983s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '77' because it was < 2 characters long 983s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '89' because it was < 2 characters long 983s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '92' because it was < 2 characters long 983s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '99' because it was < 2 characters long 983s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '108' because it was < 2 characters long 983s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '109' because it was < 2 characters long 983s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '111' because it was < 2 characters long 983s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '116' because it was < 2 characters long 983s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 983s Warning: skipping read '135' because it was < 2 characters long 983s Read 50 alignments... 983s Read 100 alignments... 983s 145 reads; of these: 983s 145 (100.00%) were unpaired; of these: 983s 145 (100.00%) aligned 0 times 983s 0 (0.00%) aligned exactly 1 time 983s 0 (0.00%) aligned >1 times 983s 0.00% overall alignment rate 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s Processing line... 983s --- Summary --- 983s Read 1 reference strings 983s Checked 0 alignments, 0 edits 983s --------------- 983s PASSED 983s Flattened IUPAC characters 983s Mutating sequence Sim.pm.2 983s Introducing 3 SNPs, 2/2 ref/read gaps, and 0 rearrangements 983s Finished SNPs 983s Finished ref gaps 983s Finished read gaps 983s Mutating sequence Sim.pm.1 983s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 983s Finished SNPs 983s Finished ref gaps 983s Finished read gaps 983s Mutated reference genome to subject genome 983s SNPs introduced: 9 983s Reference gaps introduced: 2 983s Read gaps introduced: 3 983s Rearrangements introduced: 1 983s Created read sampler 983s Sampling 104 reads 983s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 983s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 983s parsing sequence Sim.pm.1... 983s parsing sequence Sim.pm.2... 983s Parsed 110 reference bases 983s *** Run 75 of 100 983s /usr/bin/bowtie2 --large-index --rdg 27.2064441077168,14.3758218954061 --local --mm --cp-ival 1 --cp-min 4 --score-min L,3.48625924826229,3.97929479425776 --trim5 1 --rfg 31.3173760361862 -i C,4.34737578012373 -R 2 --norc --np 1 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 984s Read 50 alignments... 984s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (0) 984s Warning: skipping mate #1 of read '86' because it was < 2 characters long 984s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 984s Warning: skipping mate #1 of read '99' because it was < 2 characters long 984s 104 reads; of these: 984s 102 (98.08%) were paired; of these: 984s 102 (100.00%) aligned concordantly 0 times 984s 0 (0.00%) aligned concordantly exactly 1 time 984s 0 (0.00%) aligned concordantly >1 times 984s ---- 984s 102 pairs aligned concordantly 0 times; of these: 984s 0 (0.00%) aligned discordantly 1 time 984s ---- 984s 102 pairs aligned 0 times concordantly or discordantly; of these: 984s 204 mates make up the pairs; of these: 984s 204 (100.00%) aligned 0 times 984s 0 (0.00%) aligned exactly 1 time 984s 0 (0.00%) aligned >1 times 984s 2 (1.92%) were unpaired; of these: 984s 2 (100.00%) aligned 0 times 984s 0 (0.00%) aligned exactly 1 time 984s 0 (0.00%) aligned >1 times 984s 0.00% overall alignment rate 984s Read 100 alignments... 984s Read 150 alignments... 984s Read 200 alignments... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s /usr/bin/bowtie2 --large-index --rdg 27.2064441077168,14.3758218954061 --local --mm --cp-ival 1 --cp-min 4 --score-min L,3.48625924826229,3.97929479425776 --trim5 1 --rfg 31.3173760361862 -i C,4.34737578012373 -R 2 --norc --np 1 -f -p 2 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s --- Summary --- 984s Read 1 reference strings 984s Checked 0 alignments, 0 edits 984s --------------- 984s PASSED 984s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 984s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 984s Warning: skipping mate #1 of read '99' because it was < 2 characters long 984s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (0) 984s Warning: skipping mate #1 of read '86' because it was < 2 characters long 984s 104 reads; of these: 984s 102 (98.08%) were paired; of these: 984s 102 (100.00%) aligned concordantly 0 times 984s 0 (0.00%) aligned concordantly exactly 1 time 984s 0 (0.00%) aligned concordantly >1 times 984s ---- 984s 102 pairs aligned concordantly 0 times; of these: 984s 0 (0.00%) aligned discordantly 1 time 984s ---- 984s 102 pairs aligned 0 times concordantly or discordantly; of these: 984s 204 mates make up the pairs; of these: 984s 204 (100.00%) aligned 0 times 984s 0 (0.00%) aligned exactly 1 time 984s 0 (0.00%) aligned >1 times 984s 2 (1.92%) were unpaired; of these: 984s 2 (100.00%) aligned 0 times 984s 0 (0.00%) aligned exactly 1 time 984s 0 (0.00%) aligned >1 times 984s 0.00% overall alignment rate 984s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 984s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 984s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 984s /usr/bin/bowtie2 --large-index --rdg 27.2064441077168,14.3758218954061 --local --mm --cp-ival 1 --cp-min 4 --score-min L,3.48625924826229,3.97929479425776 --trim5 1 --rfg 31.3173760361862 -i C,4.34737578012373 -R 2 --norc --np 1 -f -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 984s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 984s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 984s Warning: skipping mate #1 of read '99' because it was < 2 characters long 984s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (0) 984s Warning: skipping mate #1 of read '86' because it was < 2 characters long 984s 104 reads; of these: 984s 102 (98.08%) were paired; of these: 984s 102 (100.00%) aligned concordantly 0 times 984s 0 (0.00%) aligned concordantly exactly 1 time 984s 0 (0.00%) aligned concordantly >1 times 984s ---- 984s 102 pairs aligned concordantly 0 times; of these: 984s 0 (0.00%) aligned discordantly 1 time 984s ---- 984s 102 pairs aligned 0 times concordantly or discordantly; of these: 984s 204 mates make up the pairs; of these: 984s 204 (100.00%) aligned 0 times 984s 0 (0.00%) aligned exactly 1 time 984s 0 (0.00%) aligned >1 times 984s 2 (1.92%) were unpaired; of these: 984s 2 (100.00%) aligned 0 times 984s 0 (0.00%) aligned exactly 1 time 984s 0 (0.00%) aligned >1 times 984s 0.00% overall alignment rate 984s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 984s Flattened IUPAC characters 984s Mutating sequence Sim.pm.2 984s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 984s Finished SNPs 984s Finished ref gaps 984s Finished read gaps 984s Mutating sequence Sim.pm.1 984s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 984s Finished SNPs 984s Finished ref gaps 984s Finished read gaps 984s Mutated reference genome to subject genome 984s SNPs introduced: 9 984s Reference gaps introduced: 1 984s Read gaps introduced: 0 984s Rearrangements introduced: 1 984s Created read sampler 984s Sampling 25 reads 984s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 984s *** Run 76 of 100 984s /usr/bin/bowtie2 --large-index -k 3 --trim3 1 --rdg 24.4341008881566 --local --cp-ival 1 --mm --cp-min 6 --score-min L,7.8262444712365,6.92050058452531 --trim5 3 --rfg 20.0903948627801,6.49474631811187 -N 1 -L13 --np 11 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 984s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 984s parsing sequence Sim.pm.1... 984s parsing sequence Sim.pm.2... 984s Parsed 110 reference bases 984s Warning: skipping read '0' because length (0) <= # seed mismatches (1) 984s Warning: skipping read '0' because it was < 2 characters long 984s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 984s Warning: skipping read '11' because it was < 2 characters long 984s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 984s Warning: skipping read '15' because it was < 2 characters long 984s 25 reads; of these: 984s 25 (100.00%) were unpaired; of these: 984s 25 (100.00%) aligned 0 times 984s 0 (0.00%) aligned exactly 1 time 984s 0 (0.00%) aligned >1 times 984s 0.00% overall alignment rate 984s /usr/bin/bowtie2 --large-index -k 3 --trim3 1 --rdg 24.4341008881566 --local --cp-ival 1 --mm --cp-min 6 --score-min L,7.8262444712365,6.92050058452531 --trim5 3 --rfg 20.0903948627801,6.49474631811187 -N 1 -L13 --np 11 -r -p 4 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s Processing line... 984s --- Summary --- 984s Read 1 reference strings 984s Checked 0 alignments, 0 edits 984s --------------- 984s PASSED 984s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 984s Warning: skipping read '0' because length (0) <= # seed mismatches (1) 984s Warning: skipping read '0' because it was < 2 characters long 984s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 984s Warning: skipping read '11' because it was < 2 characters long 984s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 984s Warning: skipping read '15' because it was < 2 characters long 985s 25 reads; of these: 985s 25 (100.00%) were unpaired; of these: 985s 25 (100.00%) aligned 0 times 985s 0 (0.00%) aligned exactly 1 time 985s 0 (0.00%) aligned >1 times 985s 0.00% overall alignment rate 985s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 985s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 985s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 985s Flattened IUPAC characters 985s Mutating sequence Sim.pm.1 985s Introducing 8 SNPs, 1/1 ref/read gaps, and 1 rearrangements 985s Finished SNPs 985s Finished ref gaps 985s Finished read gaps 985s Mutating sequence Sim.pm.2 985s Introducing 8 SNPs, 0/2 ref/read gaps, and 0 rearrangements 985s Finished SNPs 985s Finished ref gaps 985s Finished read gaps 985s Mutated reference genome to subject genome 985s SNPs introduced: 16 985s Reference gaps introduced: 1 985s Read gaps introduced: 3 985s Rearrangements introduced: 1 985s Created read sampler 985s Sampling 44 reads 985s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 985s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 985s parsing sequence Sim.pm.1... 985s parsing sequence Sim.pm.2... 985s Parsed 110 reference bases 985s *** Run 77 of 100 985s /usr/bin/bowtie2 --np 2 -D 19 --score-min L,8.8576997946503,4.26841641022609 --cp-min 2 --cp-ival 1 --trim3 8 --mp 7.8574455202943,4.2848680877191 -a --large-index -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 985s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 985s Warning: skipping read '7' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 985s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '11' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 985s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '15' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 985s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '18' because it was < 2 characters long 985s Warning: skipping mate #2 of read '18' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 985s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 985s Warning: skipping read '27' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 985s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '28' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 985s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '31' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 985s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 985s Warning: skipping mate #2 of read '36' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 985s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '40' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 985s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 985s Warning: skipping read '41' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 985s 44 reads; of these: 985s 35 (79.55%) were paired; of these: 985s 35 (100.00%) aligned concordantly 0 times 985s 0 (0.00%) aligned concordantly exactly 1 time 985s 0 (0.00%) aligned concordantly >1 times 985s ---- 985s 35 pairs aligned concordantly 0 times; of these: 985s 0 (0.00%) aligned discordantly 1 time 985s ---- 985s 35 pairs aligned 0 times concordantly or discordantly; of these: 985s 70 mates make up the pairs; of these: 985s 61 (87.14%) aligned 0 times 985s 6 (8.57%) aligned exactly 1 time 985s 3 (4.29%) aligned >1 times 985s 9 (20.45%) were unpaired; of these: 985s 9 (100.00%) aligned 0 times 985s 0 (0.00%) aligned exactly 1 time 985s 0 (0.00%) aligned >1 times 985s 11.39% overall alignment rate 985s Read 50 alignments... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s GGACAGGGGAGGCGAACAAAGGGCCTCGCA 985s GGACAGGGGAGGCGAACAAAGGGCCTCGCA 985s Processing line... 985s Processing line... 985s GAGG 985s GAGG 985s Processing line... 985s CCTC 985s CCTC 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s GACAGGGGAGGCGAACAAA 985s GACAGGGGAGGCGAACAAA 985s Processing line... 985s TA 985s TA 985s Processing line... 985s TA 985s TA 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s GATGGGACAG 985s GATGGGACAG 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s GGGACA 985s GGGACA 985s Processing line... 985s Processing line... 985s AGGC 985s AGGC 985s Processing line... 985s GCCT 985s GCCT 985s Processing line... 985s ATGGGACAGGGGAGGCGA 985s ATGGGACAGGGGAGGCGA 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s GATGGGACAGGGG 985s GATGGGACAGGGG 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s --- Summary --- 985s Read 1 reference strings 985s Checked 12 alignments, 0 edits 985s --------------- 985s PASSED 985s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 985s /usr/bin/bowtie2 --np 2 -D 19 --score-min L,8.8576997946503,4.26841641022609 --cp-min 2 --cp-ival 1 --trim3 8 --mp 7.8574455202943,4.2848680877191 -a --large-index -f -p 3 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 985s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 985s Warning: skipping read '7' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 985s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '11' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 985s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '15' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 985s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '18' because it was < 2 characters long 985s Warning: skipping mate #2 of read '18' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 985s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 985s Warning: skipping mate #2 of read '36' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 985s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 985s Warning: skipping read '27' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 985s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '28' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 985s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '31' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 985s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 985s Warning: skipping mate #1 of read '40' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 985s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 985s Warning: skipping read '41' because it was < 2 characters long 985s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 985s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 985s 44 reads; of these: 985s 35 (79.55%) were paired; of these: 985s 35 (100.00%) aligned concordantly 0 times 985s 0 (0.00%) aligned concordantly exactly 1 time 985s 0 (0.00%) aligned concordantly >1 times 985s ---- 985s 35 pairs aligned concordantly 0 times; of these: 985s 0 (0.00%) aligned discordantly 1 time 985s ---- 985s 35 pairs aligned 0 times concordantly or discordantly; of these: 985s 70 mates make up the pairs; of these: 985s 61 (87.14%) aligned 0 times 985s 6 (8.57%) aligned exactly 1 time 985s 3 (4.29%) aligned >1 times 985s 9 (20.45%) were unpaired; of these: 985s 9 (100.00%) aligned 0 times 985s 0 (0.00%) aligned exactly 1 time 985s 0 (0.00%) aligned >1 times 985s 11.39% overall alignment rate 985s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 985s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 985s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 985s Flattened IUPAC characters 985s Mutating sequence Sim.pm.1 985s Introducing 5 SNPs, 0/0 ref/read gaps, and 2 rearrangements 985s Finished SNPs 985s Finished ref gaps 985s Finished read gaps 985s Mutating sequence Sim.pm.2 985s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 985s Finished SNPs 985s Finished ref gaps 985s Finished read gaps 985s Mutated reference genome to subject genome 985s SNPs introduced: 10 985s Reference gaps introduced: 1 985s Read gaps introduced: 1 985s Rearrangements introduced: 2 985s Created read sampler 985s Sampling 47 reads 985s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 985s *** Run 78 of 100 985s /usr/bin/bowtie2 -D 39 --norc --score-min L,5.54692095913379,2.4996763781982 --rfg 48.3027855207849,16.7203351921535 --mm --cp-ival 1 --cp-min 21 --large-index -M 3 --local --rdg 38.3347682796676 --trim3 0 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 985s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 985s parsing sequence Sim.pm.1... 985s parsing sequence Sim.pm.2... 985s Parsed 110 reference bases 985s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 985s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 985s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 985s 47 reads; of these: 985s 47 (100.00%) were unpaired; of these: 985s 47 (100.00%) aligned 0 times 985s 0 (0.00%) aligned exactly 1 time 985s 0 (0.00%) aligned >1 times 985s 0.00% overall alignment rate 985s Read 50 alignments... 985s Processing line... 985s /usr/bin/bowtie2 -D 39 --norc --score-min L,5.54692095913379,2.4996763781982 --rfg 48.3027855207849,16.7203351921535 --mm --cp-ival 1 --cp-min 21 --large-index -M 3 --local --rdg 38.3347682796676 --trim3 0 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s Processing line... 985s --- Summary --- 985s Read 1 reference strings 985s Checked 0 alignments, 0 edits 985s --------------- 985s PASSED 985s ALSO checking that bowtie2 and bowtie2-align match up 986s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 986s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 986s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 986s 47 reads; of these: 986s 47 (100.00%) were unpaired; of these: 986s 47 (100.00%) aligned 0 times 986s 0 (0.00%) aligned exactly 1 time 986s 0 (0.00%) aligned >1 times 986s 0.00% overall alignment rate 986s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 986s Flattened IUPAC characters 986s Mutating sequence Sim.pm.1 986s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 986s Finished SNPs 986s Finished ref gaps 986s Finished read gaps 986s Mutating sequence Sim.pm.2 986s Introducing 5 SNPs, 1/1 ref/read gaps, and 1 rearrangements 986s Finished SNPs 986s Finished ref gaps 986s Finished read gaps 986s Mutated reference genome to subject genome 986s SNPs introduced: 8 986s Reference gaps introduced: 1 986s Read gaps introduced: 1 986s Rearrangements introduced: 1 986s Created read sampler 986s Sampling 35 reads 986s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 986s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 986s parsing sequence Sim.pm.1... 986s parsing sequence Sim.pm.2... 986s *** Run 79 of 100 986s /usr/bin/bowtie2 --score-min L,2.03929636782975,2.89307632106891 --large-index --ma 8.20707019679294 --trim5 6 -D 22 --cp-ival 3 -N 0 -L13 --np 1 --cp-min 2 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 986s Parsed 110 reference bases 986s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 986s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 986s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '2' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 986s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '5' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 986s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '10' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 986s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '17' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 986s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '20' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 986s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '21' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 986s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '27' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 986s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '30' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 986s 35 reads; of these: 986s 35 (100.00%) were unpaired; of these: 986s 31 (88.57%) aligned 0 times 986s 4 (11.43%) aligned exactly 1 time 986s 0 (0.00%) aligned >1 times 986s 11.43% overall alignment rate 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s TCCAGGGACGCAC 986s TCCAGGGACGCAC 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s ATGCAGATGGGA 986s ATGCAGATGGGA 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s TGCAGATGGGACAGGGGAGGCGAACAAAGGGCCTCG 986s TGCAGATGGGACAGGGGAGGCGAACAAAGGGCCTCG 986s Processing line... 986s Processing line... 986s Processing line... 986s CGGGAAG 986s CGGGAAG 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s --- Summary --- 986s Read 1 reference strings 986s Checked 4 alignments, 0 edits 986s --------------- 986s PASSED 986s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 986s /usr/bin/bowtie2 --score-min L,2.03929636782975,2.89307632106891 --large-index --ma 8.20707019679294 --trim5 6 -D 22 --cp-ival 3 -N 0 -L13 --np 1 --cp-min 2 -q -p 4 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 986s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 986s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 986s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '2' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 986s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '5' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 986s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '10' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 986s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '17' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 986s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '20' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 986s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '21' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 986s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '27' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 986s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 986s Warning: skipping read '30' because it was < 2 characters long 986s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 986s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 986s 35 reads; of these: 986s 35 (100.00%) were unpaired; of these: 986s 31 (88.57%) aligned 0 times 986s 4 (11.43%) aligned exactly 1 time 986s 0 (0.00%) aligned >1 times 986s 11.43% overall alignment rate 986s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 986s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 986s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 986s Flattened IUPAC characters 986s Mutating sequence Sim.pm.1 986s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 986s Finished SNPs 986s Finished ref gaps 986s Finished read gaps 986s Mutating sequence Sim.pm.2 986s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 986s Finished SNPs 986s Finished ref gaps 986s Finished read gaps 986s Mutated reference genome to subject genome 986s SNPs introduced: 4 986s Reference gaps introduced: 1 986s Read gaps introduced: 1 986s Rearrangements introduced: 0 986s Created read sampler 986s Sampling 42 reads 986s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 986s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 986s parsing sequence Sim.pm.1... 986s parsing sequence Sim.pm.2... 986s Parsed 110 reference bases 986s *** Run 80 of 100 986s /usr/bin/bowtie2 --np 1 --norc -R 1 --score-min L,2.51023304619352,8.31396240353901 --n-ceil 0.983441462550557,1.29738096929033 --cp-min 7 --cp-ival 1 --mm --local --trim3 0 --rdg 16.8591512772384,7.91760921338423 --large-index --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 986s Warning: skipping mate #2 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 986s Warning: skipping mate #2 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 986s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 986s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 986s 42 reads; of these: 986s 42 (100.00%) were paired; of these: 986s 42 (100.00%) aligned concordantly 0 times 986s 0 (0.00%) aligned concordantly exactly 1 time 986s 0 (0.00%) aligned concordantly >1 times 986s ---- 986s 42 pairs aligned concordantly 0 times; of these: 986s 0 (0.00%) aligned discordantly 1 time 986s ---- 986s 42 pairs aligned 0 times concordantly or discordantly; of these: 986s 84 mates make up the pairs; of these: 986s 84 (100.00%) aligned 0 times 986s 0 (0.00%) aligned exactly 1 time 986s 0 (0.00%) aligned >1 times 986s 0.00% overall alignment rate 986s Read 50 alignments... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s Processing line... 986s --- Summary --- 986s Read 1 reference strings 986s Checked 0 alignments, 0 edits 986s --------------- 986s PASSED 986s Flattened IUPAC characters 986s Mutating sequence Sim.pm.2 986s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 986s Finished SNPs 986s Finished ref gaps 986s Finished read gaps 986s Mutating sequence Sim.pm.1 986s Introducing 5 SNPs, 0/1 ref/read gaps, and 1 rearrangements 986s Finished SNPs 986s Finished ref gaps 986s Finished read gaps 986s Mutated reference genome to subject genome 986s SNPs introduced: 11 986s Reference gaps introduced: 0 986s Read gaps introduced: 1 986s Rearrangements introduced: 2 986s Created read sampler 986s Sampling 89 reads 986s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 986s *** Run 81 of 100 986s /usr/bin/bowtie2 -D 2 -R 2 --rfg 23.1081274427431 --score-min L,7.58689460246174,7.95759507659617 --cp-min 2 --cp-ival 1 --mm --local --trim3 9 --large-index -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 986s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 986s parsing sequence Sim.pm.1... 986s parsing sequence Sim.pm.2... 986s Parsed 110 reference bases 987s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '5' because it was < 2 characters long 987s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '9' because it was < 2 characters long 987s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '14' because it was < 2 characters long 987s Warning: skipping mate #2 of read '14' because it was < 2 characters long 987s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '17' because it was < 2 characters long 987s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '20' because it was < 2 characters long 987s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '25' because it was < 2 characters long 987s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #2 of read '29' because it was < 2 characters long 987s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 987s Warning: skipping read '41' because it was < 2 characters long 987s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '45' because it was < 2 characters long 987s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '51' because it was < 2 characters long 987s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '52' because it was < 2 characters long 987s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '61' because it was < 2 characters long 987s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '65' because it was < 2 characters long 987s Read 50 alignments... 987s Read 100 alignments... 987s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '66' because it was < 2 characters long 987s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 987s Warning: skipping read '67' because it was < 2 characters long 987s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '71' because it was < 2 characters long 987s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '73' because it was < 2 characters long 987s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '77' because it was < 2 characters long 987s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #2 of read '80' because it was < 2 characters long 987s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '86' because it was < 2 characters long 987s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '87' because it was < 2 characters long 987s 89 reads; of these: 987s 74 (83.15%) were paired; of these: 987s 74 (100.00%) aligned concordantly 0 times 987s 0 (0.00%) aligned concordantly exactly 1 time 987s 0 (0.00%) aligned concordantly >1 times 987s ---- 987s 74 pairs aligned concordantly 0 times; of these: 987s 0 (0.00%) aligned discordantly 1 time 987s ---- 987s 74 pairs aligned 0 times concordantly or discordantly; of these: 987s 148 mates make up the pairs; of these: 987s 148 (100.00%) aligned 0 times 987s 0 (0.00%) aligned exactly 1 time 987s 0 (0.00%) aligned >1 times 987s 15 (16.85%) were unpaired; of these: 987s 15 (100.00%) aligned 0 times 987s 0 (0.00%) aligned exactly 1 time 987s 0 (0.00%) aligned >1 times 987s 0.00% overall alignment rate 987s Read 150 alignments... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s /usr/bin/bowtie2 -D 2 -R 2 --rfg 23.1081274427431 --score-min L,7.58689460246174,7.95759507659617 --cp-min 2 --cp-ival 1 --mm --local --trim3 9 --large-index -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s --- Summary --- 987s Read 1 reference strings 987s Checked 0 alignments, 0 edits 987s --------------- 987s PASSED 987s ALSO checking that bowtie2 and bowtie2-align match up 987s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '5' because it was < 2 characters long 987s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '9' because it was < 2 characters long 987s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '14' because it was < 2 characters long 987s Warning: skipping mate #2 of read '14' because it was < 2 characters long 987s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '17' because it was < 2 characters long 987s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '20' because it was < 2 characters long 987s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '25' because it was < 2 characters long 987s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #2 of read '29' because it was < 2 characters long 987s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 987s Warning: skipping read '41' because it was < 2 characters long 987s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '45' because it was < 2 characters long 987s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '51' because it was < 2 characters long 987s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '52' because it was < 2 characters long 987s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '61' because it was < 2 characters long 987s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '65' because it was < 2 characters long 987s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '66' because it was < 2 characters long 987s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 987s Warning: skipping read '67' because it was < 2 characters long 987s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '71' because it was < 2 characters long 987s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '73' because it was < 2 characters long 987s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '77' because it was < 2 characters long 987s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #2 of read '80' because it was < 2 characters long 987s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '86' because it was < 2 characters long 987s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '87' because it was < 2 characters long 987s 89 reads; of these: 987s 74 (83.15%) were paired; of these: 987s 74 (100.00%) aligned concordantly 0 times 987s 0 (0.00%) aligned concordantly exactly 1 time 987s 0 (0.00%) aligned concordantly >1 times 987s ---- 987s 74 pairs aligned concordantly 0 times; of these: 987s 0 (0.00%) aligned discordantly 1 time 987s ---- 987s 74 pairs aligned 0 times concordantly or discordantly; of these: 987s 148 mates make up the pairs; of these: 987s 148 (100.00%) aligned 0 times 987s 0 (0.00%) aligned exactly 1 time 987s 0 (0.00%) aligned >1 times 987s 15 (16.85%) were unpaired; of these: 987s 15 (100.00%) aligned 0 times 987s 0 (0.00%) aligned exactly 1 time 987s 0 (0.00%) aligned >1 times 987s 0.00% overall alignment rate 987s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 987s /usr/bin/bowtie2 -D 2 -R 2 --rfg 23.1081274427431 --score-min L,7.58689460246174,7.95759507659617 --cp-min 2 --cp-ival 1 --mm --local --trim3 9 --large-index -q -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 987s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 987s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '5' because it was < 2 characters long 987s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '9' because it was < 2 characters long 987s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '14' because it was < 2 characters long 987s Warning: skipping mate #2 of read '14' because it was < 2 characters long 987s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '17' because it was < 2 characters long 987s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '20' because it was < 2 characters long 987s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '25' because it was < 2 characters long 987s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #2 of read '29' because it was < 2 characters long 987s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '51' because it was < 2 characters long 987s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '52' because it was < 2 characters long 987s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '61' because it was < 2 characters long 987s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 987s Warning: skipping read '41' because it was < 2 characters long 987s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '45' because it was < 2 characters long 987s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '65' because it was < 2 characters long 987s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '66' because it was < 2 characters long 987s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 987s Warning: skipping read '67' because it was < 2 characters long 987s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '86' because it was < 2 characters long 987s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '87' because it was < 2 characters long 987s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '71' because it was < 2 characters long 987s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '73' because it was < 2 characters long 987s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 987s Warning: skipping mate #1 of read '77' because it was < 2 characters long 987s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 987s Warning: skipping mate #2 of read '80' because it was < 2 characters long 987s 89 reads; of these: 987s 74 (83.15%) were paired; of these: 987s 74 (100.00%) aligned concordantly 0 times 987s 0 (0.00%) aligned concordantly exactly 1 time 987s 0 (0.00%) aligned concordantly >1 times 987s ---- 987s 74 pairs aligned concordantly 0 times; of these: 987s 0 (0.00%) aligned discordantly 1 time 987s ---- 987s 74 pairs aligned 0 times concordantly or discordantly; of these: 987s 148 mates make up the pairs; of these: 987s 148 (100.00%) aligned 0 times 987s 0 (0.00%) aligned exactly 1 time 987s 0 (0.00%) aligned >1 times 987s 15 (16.85%) were unpaired; of these: 987s 15 (100.00%) aligned 0 times 987s 0 (0.00%) aligned exactly 1 time 987s 0 (0.00%) aligned >1 times 987s 0.00% overall alignment rate 987s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 987s Flattened IUPAC characters 987s Mutating sequence Sim.pm.2 987s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 987s Finished SNPs 987s Finished ref gaps 987s Finished read gaps 987s Mutating sequence Sim.pm.1 987s Introducing 8 SNPs, 1/0 ref/read gaps, and 1 rearrangements 987s Finished SNPs 987s Finished ref gaps 987s Finished read gaps 987s Mutated reference genome to subject genome 987s SNPs introduced: 14 987s Reference gaps introduced: 1 987s Read gaps introduced: 0 987s Rearrangements introduced: 1 987s Created read sampler 987s Sampling 76 reads 987s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 987s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 987s parsing sequence Sim.pm.1... 987s parsing sequence Sim.pm.2... 987s Parsed 110 reference bases 987s *** Run 82 of 100 987s /usr/bin/bowtie2 -a --rdg 14.5605429306841 --large-index --cp-min 6 --cp-ival 3 --mm --trim5 0 --score-min L,3.46791598469618,4.79447447253872 --gbar 1 --n-ceil 1.33915181100737,0.632185154937086 --norc -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 987s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 987s 76 reads; of these: 987s 76 (100.00%) were unpaired; of these: 987s 69 (90.79%) aligned 0 times 987s 5 (6.58%) aligned exactly 1 time 987s 2 (2.63%) aligned >1 times 987s 9.21% overall alignment rate 987s Read 50 alignments... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s AGGGGAG 987s AGGGGAG 987s Processing line... 987s Processing line... 987s Processing line... 987s CCT 987s CCT 987s Processing line... 987s CTCGCAGC 987s CTCGCAGC 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s GC 987s GC 987s Processing line... 987s Processing line... 987s Processing line... 987s TGGGAC 987s TGGGAC 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s GT 987s GT 987s Processing line... 987s GT 987s GT 987s Processing line... 987s GT 987s GT 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s Processing line... 987s /usr/bin/bowtie2 -a --rdg 14.5605429306841 --large-index --cp-min 6 --cp-ival 3 --mm --trim5 0 --score-min L,3.46791598469618,4.79447447253872 --gbar 1 --n-ceil 1.33915181100737,0.632185154937086 --norc -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 987s Processing line... 987s TGCAG 987s TGCAG 987s Processing line... 987s Processing line... 987s --- Summary --- 987s Read 1 reference strings 987s Checked 21 alignments, 0 edits 987s --------------- 987s PASSED 987s ALSO checking that bowtie2 and bowtie2-align match up 987s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 987s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 987s 76 reads; of these: 987s 76 (100.00%) were unpaired; of these: 987s 69 (90.79%) aligned 0 times 987s 5 (6.58%) aligned exactly 1 time 987s 2 (2.63%) aligned >1 times 987s 9.21% overall alignment rate 987s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 987s /usr/bin/bowtie2 -a --rdg 14.5605429306841 --large-index --cp-min 6 --cp-ival 3 --mm --trim5 0 --score-min L,3.46791598469618,4.79447447253872 --gbar 1 --n-ceil 1.33915181100737,0.632185154937086 --norc -r -p 4 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 987s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 988s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 988s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 988s 76 reads; of these: 988s 76 (100.00%) were unpaired; of these: 988s 69 (90.79%) aligned 0 times 988s 5 (6.58%) aligned exactly 1 time 988s 2 (2.63%) aligned >1 times 988s 9.21% overall alignment rate 988s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 988s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 988s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 988s Flattened IUPAC characters 988s Mutating sequence Sim.pm.2 988s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 988s Finished SNPs 988s Finished ref gaps 988s Finished read gaps 988s Mutating sequence Sim.pm.1 988s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 988s Finished SNPs 988s Finished ref gaps 988s Finished read gaps 988s Mutated reference genome to subject genome 988s SNPs introduced: 7 988s Reference gaps introduced: 0 988s Read gaps introduced: 0 988s Rearrangements introduced: 1 988s Created read sampler 988s Sampling 101 reads 988s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 988s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 988s parsing sequence Sim.pm.1... 988s parsing sequence Sim.pm.2... 988s Parsed 110 reference bases 988s *** Run 83 of 100 988s /usr/bin/bowtie2 -M 10 --large-index --mp 9.89661042728084,8.95719666050827 --trim3 7 --local --cp-ival 2 --cp-min 2 --n-ceil 0.0850852284264958,0.0292335271299117 --score-min L,2.83599596473372,4.40512153060889 --trim5 7 -D 28 -R 3 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 988s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 988s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '7' because it was < 2 characters long 988s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '8' because it was < 2 characters long 988s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '21' because it was < 2 characters long 988s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '23' because it was < 2 characters long 988s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '27' because it was < 2 characters long 988s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '31' because it was < 2 characters long 988s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '32' because it was < 2 characters long 988s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '35' because it was < 2 characters long 988s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '41' because it was < 2 characters long 988s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '43' because it was < 2 characters long 988s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 988s Warning: skipping mate #2 of read '44' because it was < 2 characters long 988s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '45' because it was < 2 characters long 988s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '46' because it was < 2 characters long 988s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '50' because it was < 2 characters long 988s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 988s Warning: skipping mate #2 of read '59' because it was < 2 characters long 988s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '60' because it was < 2 characters long 988s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '63' because it was < 2 characters long 988s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '71' because it was < 2 characters long 988s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '74' because it was < 2 characters long 988s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '75' because it was < 2 characters long 988s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '81' because it was < 2 characters long 988s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 988s Read 50 alignments... 988s Warning: skipping mate #1 of read '82' because it was < 2 characters long 988s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '83' because it was < 2 characters long 988s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '85' because it was < 2 characters long 988s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '86' because it was < 2 characters long 988s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '87' because it was < 2 characters long 988s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '91' because it was < 2 characters long 988s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '93' because it was < 2 characters long 988s Warning: skipping mate #2 of read '95' because length (1) <= # seed mismatches (0) 988s Warning: skipping mate #2 of read '95' because it was < 2 characters long 988s Read 100 alignments... 988s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '97' because it was < 2 characters long 988s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '99' because it was < 2 characters long 988s 101 reads; of these: 988s 68 (67.33%) were paired; of these: 988s 68 (100.00%) aligned concordantly 0 times 988s 0 (0.00%) aligned concordantly exactly 1 time 988s 0 (0.00%) aligned concordantly >1 times 988s ---- 988s 68 pairs aligned concordantly 0 times; of these: 988s 0 (0.00%) aligned discordantly 1 time 988s ---- 988s 68 pairs aligned 0 times concordantly or discordantly; of these: 988s 136 mates make up the pairs; of these: 988s 136 (100.00%) aligned 0 times 988s 0 (0.00%) aligned exactly 1 time 988s 0 (0.00%) aligned >1 times 988s 33 (32.67%) were unpaired; of these: 988s 33 (100.00%) aligned 0 times 988s 0 (0.00%) aligned exactly 1 time 988s 0 (0.00%) aligned >1 times 988s 0.00% overall alignment rate 988s Read 150 alignments... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s Processing line... 988s --- Summary --- 988s Read 1 reference strings 988s Checked 0 alignments, 0 edits 988s --------------- 988s PASSED 988s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 988s /usr/bin/bowtie2 -M 10 --large-index --mp 9.89661042728084,8.95719666050827 --trim3 7 --local --cp-ival 2 --cp-min 2 --n-ceil 0.0850852284264958,0.0292335271299117 --score-min L,2.83599596473372,4.40512153060889 --trim5 7 -D 28 -R 3 -f -p 4 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 988s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 988s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '7' because it was < 2 characters long 988s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '8' because it was < 2 characters long 988s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '21' because it was < 2 characters long 988s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '23' because it was < 2 characters long 988s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '27' because it was < 2 characters long 988s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '31' because it was < 2 characters long 988s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '32' because it was < 2 characters long 988s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '50' because it was < 2 characters long 988s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 988s Warning: skipping mate #2 of read '59' because it was < 2 characters long 988s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '60' because it was < 2 characters long 988s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '63' because it was < 2 characters long 988s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '35' because it was < 2 characters long 988s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '41' because it was < 2 characters long 988s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '43' because it was < 2 characters long 988s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 988s Warning: skipping mate #2 of read '44' because it was < 2 characters long 988s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '45' because it was < 2 characters long 988s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '46' because it was < 2 characters long 988s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '81' because it was < 2 characters long 988s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '82' because it was < 2 characters long 988s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '83' because it was < 2 characters long 988s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '85' because it was < 2 characters long 988s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '86' because it was < 2 characters long 988s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '87' because it was < 2 characters long 988s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 988s Warning: skipping read '91' because it was < 2 characters long 988s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '93' because it was < 2 characters long 988s Warning: skipping mate #2 of read '95' because length (1) <= # seed mismatches (0) 988s Warning: skipping mate #2 of read '95' because it was < 2 characters long 988s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '71' because it was < 2 characters long 988s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '74' because it was < 2 characters long 988s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '75' because it was < 2 characters long 988s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '97' because it was < 2 characters long 988s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (0) 988s Warning: skipping mate #1 of read '99' because it was < 2 characters long 988s 101 reads; of these: 988s 68 (67.33%) were paired; of these: 988s 68 (100.00%) aligned concordantly 0 times 988s 0 (0.00%) aligned concordantly exactly 1 time 988s 0 (0.00%) aligned concordantly >1 times 988s ---- 988s 68 pairs aligned concordantly 0 times; of these: 988s 0 (0.00%) aligned discordantly 1 time 988s ---- 988s 68 pairs aligned 0 times concordantly or discordantly; of these: 988s 136 mates make up the pairs; of these: 988s 136 (100.00%) aligned 0 times 988s 0 (0.00%) aligned exactly 1 time 988s 0 (0.00%) aligned >1 times 988s 33 (32.67%) were unpaired; of these: 988s 33 (100.00%) aligned 0 times 988s 0 (0.00%) aligned exactly 1 time 988s 0 (0.00%) aligned >1 times 988s 0.00% overall alignment rate 988s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 988s Flattened IUPAC characters 988s Mutating sequence Sim.pm.2 988s Introducing 8 SNPs, 3/0 ref/read gaps, and 1 rearrangements 988s Finished SNPs 988s *** Run 84 of 100 988s /usr/bin/bowtie2 --mm --cp-ival 3 --cp-min 3 --large-index --rdg 43.6809615352572 --mp 6.77100324190002,5.22060809133187 -a --local -D 5 --score-min L,6.5580642104314,5.40266311086079 --trim5 4 --rfg 38.4441683538045,4.37775960802546 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 988s Finished ref gaps 988s Finished read gaps 988s Mutating sequence Sim.pm.1 988s Introducing 4 SNPs, 0/2 ref/read gaps, and 1 rearrangements 988s Finished SNPs 988s Finished ref gaps 988s Finished read gaps 988s Mutated reference genome to subject genome 988s SNPs introduced: 12 988s Reference gaps introduced: 3 988s Read gaps introduced: 2 988s Rearrangements introduced: 2 988s Created read sampler 988s Sampling 85 reads 988s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 988s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 988s parsing sequence Sim.pm.1... 988s parsing sequence Sim.pm.2... 988s Parsed 110 reference bases 989s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '0' because it was < 2 characters long 989s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '8' because it was < 2 characters long 989s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '21' because it was < 2 characters long 989s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 989s Warning: skipping read '39' because it was < 2 characters long 989s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 989s Warning: skipping read '41' because it was < 2 characters long 989s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '42' because it was < 2 characters long 989s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '45' because it was < 2 characters long 989s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '48' because it was < 2 characters long 989s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '50' because it was < 2 characters long 989s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '54' because it was < 2 characters long 989s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '55' because it was < 2 characters long 989s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '76' because it was < 2 characters long 989s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 989s Warning: skipping read '78' because it was < 2 characters long 989s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '80' because it was < 2 characters long 989s 85 reads; of these: 989s 85 (100.00%) were unpaired; of these: 989s 85 (100.00%) aligned 0 times 989s 0 (0.00%) aligned exactly 1 time 989s 0 (0.00%) aligned >1 times 989s 0.00% overall alignment rate 989s Read 50 alignments... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s /usr/bin/bowtie2 --mm --cp-ival 3 --cp-min 3 --large-index --rdg 43.6809615352572 --mp 6.77100324190002,5.22060809133187 -a --local -D 5 --score-min L,6.5580642104314,5.40266311086079 --trim5 4 --rfg 38.4441683538045,4.37775960802546 -r -p 2 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s --- Summary --- 989s Read 1 reference strings 989s Checked 0 alignments, 0 edits 989s --------------- 989s PASSED 989s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 989s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '0' because it was < 2 characters long 989s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '8' because it was < 2 characters long 989s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '21' because it was < 2 characters long 989s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 989s Warning: skipping read '39' because it was < 2 characters long 989s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 989s Warning: skipping read '41' because it was < 2 characters long 989s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '42' because it was < 2 characters long 989s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '45' because it was < 2 characters long 989s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '48' because it was < 2 characters long 989s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '50' because it was < 2 characters long 989s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '54' because it was < 2 characters long 989s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '55' because it was < 2 characters long 989s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '80' because it was < 2 characters long 989s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '76' because it was < 2 characters long 989s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 989s Warning: skipping read '78' because it was < 2 characters long 989s 85 reads; of these: 989s 85 (100.00%) were unpaired; of these: 989s 85 (100.00%) aligned 0 times 989s 0 (0.00%) aligned exactly 1 time 989s 0 (0.00%) aligned >1 times 989s 0.00% overall alignment rate 989s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 989s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 989s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 989s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 989s /usr/bin/bowtie2 --mm --cp-ival 3 --cp-min 3 --large-index --rdg 43.6809615352572 --mp 6.77100324190002,5.22060809133187 -a --local -D 5 --score-min L,6.5580642104314,5.40266311086079 --trim5 4 --rfg 38.4441683538045,4.37775960802546 -r -p 4 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 989s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '0' because it was < 2 characters long 989s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '8' because it was < 2 characters long 989s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '21' because it was < 2 characters long 989s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 989s Warning: skipping read '39' because it was < 2 characters long 989s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 989s Warning: skipping read '41' because it was < 2 characters long 989s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '42' because it was < 2 characters long 989s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '45' because it was < 2 characters long 989s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '76' because it was < 2 characters long 989s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 989s Warning: skipping read '78' because it was < 2 characters long 989s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '80' because it was < 2 characters long 989s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '48' because it was < 2 characters long 989s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '50' because it was < 2 characters long 989s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '54' because it was < 2 characters long 989s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '55' because it was < 2 characters long 989s 85 reads; of these: 989s 85 (100.00%) were unpaired; of these: 989s 85 (100.00%) aligned 0 times 989s 0 (0.00%) aligned exactly 1 time 989s 0 (0.00%) aligned >1 times 989s 0.00% overall alignment rate 989s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 989s Flattened IUPAC characters 989s Mutating sequence Sim.pm.1 989s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 989s Finished SNPs 989s Finished ref gaps 989s Finished read gaps 989s Mutating sequence Sim.pm.2 989s Introducing 2 SNPs, 2/4 ref/read gaps, and 1 rearrangements 989s Finished SNPs 989s Finished ref gaps 989s Finished read gaps 989s Mutated reference genome to subject genome 989s SNPs introduced: 3 989s Reference gaps introduced: 2 989s Read gaps introduced: 5 989s Rearrangements introduced: 1 989s Created read sampler 989s Sampling 12 reads 989s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 989s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 989s parsing sequence Sim.pm.1... 989s parsing sequence Sim.pm.2... 989s Parsed 110 reference bases 989s *** Run 85 of 100 989s /usr/bin/bowtie2 --large-index --trim3 5 --mp 2.73785934351294,2.6735559321252 -a --cp-ival 2 --mm --cp-min 2 --score-min L,2.40866550651219,1.48060352348317 --trim5 3 -R 1 --np 5 --norc -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 989s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 989s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '6' because it was < 2 characters long 989s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 989s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '10' because it was < 2 characters long 989s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 989s 12 reads; of these: 989s 12 (100.00%) were unpaired; of these: 989s 12 (100.00%) aligned 0 times 989s 0 (0.00%) aligned exactly 1 time 989s 0 (0.00%) aligned >1 times 989s 0.00% overall alignment rate 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s Processing line... 989s --- Summary --- 989s Read 1 reference strings 989s Checked 0 alignments, 0 edits 989s --------------- 989s PASSED 989s ALSO checking that bowtie2 and bowtie2-align match up 989s /usr/bin/bowtie2 --large-index --trim3 5 --mp 2.73785934351294,2.6735559321252 -a --cp-ival 2 --mm --cp-min 2 --score-min L,2.40866550651219,1.48060352348317 --trim5 3 -R 1 --np 5 --norc -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 989s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 989s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '6' because it was < 2 characters long 989s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 989s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 989s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 989s Warning: skipping read '10' because it was < 2 characters long 989s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 989s 12 reads; of these: 989s 12 (100.00%) were unpaired; of these: 989s 12 (100.00%) aligned 0 times 989s 0 (0.00%) aligned exactly 1 time 989s 0 (0.00%) aligned >1 times 989s 0.00% overall alignment rate 989s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 989s Flattened IUPAC characters 989s Mutating sequence Sim.pm.2 989s Introducing 2 SNPs, 1/1 ref/read gaps, and 1 rearrangements 989s Finished SNPs 989s Finished ref gaps 990s *** Run 86 of 100 990s /usr/bin/bowtie2 --cp-min 7 --nofw --norc --cp-ival 1 --mm --rdg 24.7095791712935 --rfg 46.2914170761455 --local --large-index -k 11 --score-min L,8.70724209124017,4.23418117915532 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 990s Finished read gaps 990s Mutating sequence Sim.pm.1 990s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 990s Finished SNPs 990s Finished ref gaps 990s Finished read gaps 990s Mutated reference genome to subject genome 990s SNPs introduced: 3 990s Reference gaps introduced: 1 990s Read gaps introduced: 1 990s Rearrangements introduced: 2 990s Created read sampler 990s Sampling 50 reads 990s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 990s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 990s parsing sequence Sim.pm.1... 990s parsing sequence Sim.pm.2... 990s Parsed 110 reference bases 990s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 990s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 990s 50 reads; of these: 990s 50 (100.00%) were unpaired; of these: 990s 50 (100.00%) aligned 0 times 990s 0 (0.00%) aligned exactly 1 time 990s 0 (0.00%) aligned >1 times 990s 0.00% overall alignment rate 990s Read 50 alignments... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s /usr/bin/bowtie2 --cp-min 7 --nofw --norc --cp-ival 1 --mm --rdg 24.7095791712935 --rfg 46.2914170761455 --local --large-index -k 11 --score-min L,8.70724209124017,4.23418117915532 --qseq -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s --- Summary --- 990s Read 1 reference strings 990s Checked 0 alignments, 0 edits 990s --------------- 990s PASSED 990s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 990s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 990s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 990s 50 reads; of these: 990s 50 (100.00%) were unpaired; of these: 990s 50 (100.00%) aligned 0 times 990s 0 (0.00%) aligned exactly 1 time 990s 0 (0.00%) aligned >1 times 990s 0.00% overall alignment rate 990s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 990s Flattened IUPAC characters 990s Mutating sequence Sim.pm.1 990s Introducing 9 SNPs, 1/1 ref/read gaps, and 0 rearrangements 990s Finished SNPs 990s Finished ref gaps 990s Finished read gaps 990s Mutating sequence Sim.pm.2 990s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 990s Finished SNPs 990s Finished ref gaps 990s Finished read gaps 990s Mutated reference genome to subject genome 990s SNPs introduced: 13 990s Reference gaps introduced: 1 990s Read gaps introduced: 1 990s Rearrangements introduced: 1 990s Created read sampler 990s Sampling 156 reads 990s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 990s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 990s parsing sequence Sim.pm.1... 990s *** Run 87 of 100 990s /usr/bin/bowtie2 --large-index --ma 11.6815671822677 --mp 5.34115953184597,5.28398716735603 -a --trim3 9 --rdg 20.9178077802126,14.6292864012017 --cp-ival 2 --cp-min 7 --score-min L,8.248356779623,2.37565815305847 --trim5 3 --np 2 -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 990s parsing sequence Sim.pm.2... 990s Parsed 110 reference bases 990s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 990s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 990s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 990s Warning: skipping read '1' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 990s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '2' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 990s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '3' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 990s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '6' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 990s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '9' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 990s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '10' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 990s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '14' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 990s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '15' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 990s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '17' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 990s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 990s Warning: skipping read '19' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 990s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '23' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 990s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '30' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 990s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '34' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 990s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '37' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 990s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '38' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 990s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '39' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 990s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '42' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 990s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '43' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 990s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '45' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 990s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '46' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 990s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '47' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 990s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '48' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 990s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '49' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 990s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 990s Warning: skipping read '51' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 990s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '52' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 990s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '54' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 990s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '64' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 990s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '66' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 990s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '69' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 990s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '72' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 990s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '78' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 990s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '80' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 990s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '81' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 990s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '82' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 990s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '85' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 990s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '92' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 990s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '93' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 990s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '95' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 990s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '97' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 990s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '98' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 990s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '105' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 990s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '107' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 990s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '108' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 990s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '109' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 990s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '110' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 990s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '112' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 990s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '113' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 990s Warning: skipping read '118' because length (1) <= # seed mismatches (0) 990s Warning: skipping read '118' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 990s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '120' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 990s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '121' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 990s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '123' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 990s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '124' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 990s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '125' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 990s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '129' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 990s Warning: skipping read '131' because length (1) <= # seed mismatches (0) 990s Warning: skipping read '131' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 990s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '133' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 990s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '134' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 990s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '135' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 990s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '137' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 990s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '138' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 990s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '141' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 990s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '142' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 990s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '145' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 990s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '154' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 990s Warning: skipping read '155' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '155' because it was < 2 characters long 990s 156 reads; of these: 990s 156 (100.00%) were unpaired; of these: 990s 145 (92.95%) aligned 0 times 990s 5 (3.21%) aligned exactly 1 time 990s 6 (3.85%) aligned >1 times 990s 7.05% overall alignment rate 990s Read 50 alignments... 990s Read 100 alignments... 990s Read 150 alignments... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s GGG 990s GGG 990s Processing line... 990s GGG 990s GGG 990s Processing line... 990s GGG 990s GGG 990s Processing line... 990s GGG 990s GGG 990s Processing line... 990s GGG 990s GGG 990s Processing line... 990s GGG 990s GGG 990s Processing line... 990s GGG 990s GGG 990s Processing line... 990s GGG 990s GGG 990s Processing line... 990s /usr/bin/bowtie2 --large-index --ma 11.6815671822677 --mp 5.34115953184597,5.28398716735603 -a --trim3 9 --rdg 20.9178077802126,14.6292864012017 --cp-ival 2 --cp-min 7 --score-min L,8.248356779623,2.37565815305847 --trim5 3 --np 2 -r -p 3 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s CA 990s CA 990s Processing line... 990s CA 990s CA 990s Processing line... 990s CA 990s CA 990s Processing line... 990s CA 990s CA 990s Processing line... 990s CA 990s CA 990s Processing line... 990s CA 990s CA 990s Processing line... 990s CA 990s CA 990s Processing line... 990s TG 990s TG 990s Processing line... 990s CA 990s CA 990s Processing line... 990s CA 990s CA 990s Processing line... 990s TG 990s TG 990s Processing line... 990s TG 990s TG 990s Processing line... 990s TG 990s TG 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s AGCGGAAGC 990s AGCGGAAGC 990s Processing line... 990s AAC 990s AAC 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s ACG 990s ACG 990s Processing line... 990s CGT 990s CGT 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s GCGT 990s GCGT 990s Processing line... 990s ACGC 990s ACGC 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s TGCAGATGG 990s TGCAGATGG 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s CTCG 990s CTCG 990s Processing line... 990s CTCG 990s CTCG 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s AGGCGAACAAAGGGCCTC 990s AGGCGAACAAAGGGCCTC 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s CTCGCAGCGGAAGC 990s CTCGCAGCGGAAGC 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s AA 990s AA 990s Processing line... 990s AA 990s AA 990s Processing line... 990s AA 990s AA 990s Processing line... 990s AA 990s AA 990s Processing line... 990s AA 990s AA 990s Processing line... 990s AA 990s AA 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s Processing line... 990s --- Summary --- 990s Read 1 reference strings 990s Checked 38 alignments, 0 edits 990s --------------- 990s PASSED 990s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 990s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 990s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 990s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 990s Warning: skipping read '1' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 990s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '2' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 990s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '3' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 990s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '6' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 990s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '9' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 990s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '10' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 990s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '14' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 990s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '15' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 990s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '34' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 990s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '37' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 990s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '38' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 990s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '39' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 990s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '42' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 990s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '43' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 990s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '45' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 990s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '46' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 990s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '47' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 990s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '48' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 990s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '49' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 990s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 990s Warning: skipping read '51' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 990s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '17' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 990s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 990s Warning: skipping read '19' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 990s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '64' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 990s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '66' because it was < 2 characters long 990s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '52' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 990s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '54' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 990s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '80' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 990s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '81' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 990s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '82' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 990s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '85' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 990s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '92' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 990s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '93' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 990s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '95' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 990s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '97' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 990s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '98' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 990s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '105' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 990s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '107' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 990s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '108' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 990s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '109' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 990s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '110' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 990s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '112' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 990s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '113' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 990s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '69' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 990s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '72' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 990s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '23' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 990s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '30' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 990s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '129' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 990s Warning: skipping read '131' because length (1) <= # seed mismatches (0) 990s Warning: skipping read '131' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 990s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '133' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 990s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '134' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 990s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '135' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 990s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '137' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 990s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '138' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 990s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '141' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 990s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '142' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 990s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '145' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 990s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '154' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 990s Warning: skipping read '155' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '155' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 990s Warning: skipping read '118' because length (1) <= # seed mismatches (0) 990s Warning: skipping read '118' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 990s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '120' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 990s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '121' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 990s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '123' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 990s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '124' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 990s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '125' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 990s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 990s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 990s Warning: skipping read '78' because it was < 2 characters long 990s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 991s 156 reads; of these: 991s 156 (100.00%) were unpaired; of these: 991s 145 (92.95%) aligned 0 times 991s 5 (3.21%) aligned exactly 1 time 991s 6 (3.85%) aligned >1 times 991s 7.05% overall alignment rate 991s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 991s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 991s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 991s *** Run 88 of 100 991s /usr/bin/bowtie2 -D 48 --nofw --np 3 --score-min L,6.53645952725739,8.32000591103011 --trim5 8 --cp-ival 1 --cp-min 4 --large-index --trim3 4 --rdg 29.9335791363168 --local -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 991s Flattened IUPAC characters 991s Mutating sequence Sim.pm.1 991s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 991s Finished SNPs 991s Finished ref gaps 991s Finished read gaps 991s Mutating sequence Sim.pm.2 991s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 991s Finished SNPs 991s Finished ref gaps 991s Finished read gaps 991s Mutated reference genome to subject genome 991s SNPs introduced: 11 991s Reference gaps introduced: 0 991s Read gaps introduced: 1 991s Rearrangements introduced: 0 991s Created read sampler 991s Sampling 15 reads 991s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 991s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 991s parsing sequence Sim.pm.1... 991s parsing sequence Sim.pm.2... 991s Parsed 110 reference bases 991s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 991s Warning: skipping read '3' because it was < 2 characters long 991s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 991s Warning: skipping read '4' because it was < 2 characters long 991s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 991s Warning: skipping read '10' because it was < 2 characters long 991s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 991s Warning: skipping read '14' because it was < 2 characters long 991s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 991s Warning: skipping read '15' because it was < 2 characters long 991s 15 reads; of these: 991s 15 (100.00%) were unpaired; of these: 991s 15 (100.00%) aligned 0 times 991s 0 (0.00%) aligned exactly 1 time 991s 0 (0.00%) aligned >1 times 991s 0.00% overall alignment rate 991s Processing line... 991s /usr/bin/bowtie2 -D 48 --nofw --np 3 --score-min L,6.53645952725739,8.32000591103011 --trim5 8 --cp-ival 1 --cp-min 4 --large-index --trim3 4 --rdg 29.9335791363168 --local -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s --- Summary --- 991s Read 1 reference strings 991s Checked 0 alignments, 0 edits 991s --------------- 991s PASSED 991s ALSO checking that bowtie2 and bowtie2-align match up 991s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 991s Warning: skipping read '3' because it was < 2 characters long 991s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 991s Warning: skipping read '4' because it was < 2 characters long 991s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 991s Warning: skipping read '10' because it was < 2 characters long 991s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 991s Warning: skipping read '14' because it was < 2 characters long 991s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 991s Warning: skipping read '15' because it was < 2 characters long 991s 15 reads; of these: 991s 15 (100.00%) were unpaired; of these: 991s 15 (100.00%) aligned 0 times 991s 0 (0.00%) aligned exactly 1 time 991s 0 (0.00%) aligned >1 times 991s 0.00% overall alignment rate 991s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 991s Flattened IUPAC characters 991s Mutating sequence Sim.pm.2 991s Introducing 3 SNPs, 1/5 ref/read gaps, and 1 rearrangements 991s Finished SNPs 991s Finished ref gaps 991s Finished read gaps 991s Mutating sequence Sim.pm.1 991s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 991s Finished SNPs 991s Finished ref gaps 991s Finished read gaps 991s Mutated reference genome to subject genome 991s SNPs introduced: 13 991s Reference gaps introduced: 1 991s Read gaps introduced: 5 991s Rearrangements introduced: 1 991s Created read sampler 991s Sampling 18 reads 991s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 991s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 991s parsing sequence Sim.pm.1... 991s parsing sequence Sim.pm.2... 991s Parsed 110 reference bases 991s *** Run 89 of 100 991s /usr/bin/bowtie2 -R 3 --norc --np 2 --gbar 1 --score-min L,8.50494062151758,1.88044430959866 --trim5 2 --cp-ival 1 --cp-min 4 --large-index --mp 8.66149473899373,6.45000119425827 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 991s 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 991s 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 991s 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 991s 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 991s 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 991s 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 991s 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 991s 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 991s 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 991s 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 991s 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 991s 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 991s 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 991s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 991s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 991s 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 991s 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 991s 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 991s 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 991s 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 991s 18 reads; of these: 991s 18 (100.00%) were unpaired; of these: 991s 15 (83.33%) aligned 0 times 991s 3 (16.67%) aligned exactly 1 time 991s 0 (0.00%) aligned >1 times 991s 16.67% overall alignment rate 991s Processing line... 991s /usr/bin/bowtie2 -R 3 --norc --np 2 --gbar 1 --score-min L,8.50494062151758,1.88044430959866 --trim5 2 --cp-ival 1 --cp-min 4 --large-index --mp 8.66149473899373,6.45000119425827 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s AAGGGCCTCG 991s AAGGGCCTCG 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s GAG 991s GAG 991s Processing line... 991s CAAAGGGCCTCGCAGCGGA 991s CAAAGGGCCTCGCAGCGGA 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s Processing line... 991s --- Summary --- 991s Read 1 reference strings 991s Checked 3 alignments, 0 edits 991s --------------- 991s PASSED 991s ALSO checking that bowtie2 and bowtie2-align match up 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 992s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 992s 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 992s 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 992s 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 992s 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 992s 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 992s 18 reads; of these: 992s 18 (100.00%) were unpaired; of these: 992s 15 (83.33%) aligned 0 times 992s 3 (16.67%) aligned exactly 1 time 992s 0 (0.00%) aligned >1 times 992s 16.67% overall alignment rate 992s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 992s /usr/bin/bowtie2 -R 3 --norc --np 2 --gbar 1 --score-min L,8.50494062151758,1.88044430959866 --trim5 2 --cp-ival 1 --cp-min 4 --large-index --mp 8.66149473899373,6.45000119425827 --qseq -p 4 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 992s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s 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 992s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 992s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 992s 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 992s 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 992s 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 992s 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 992s 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 992s 18 reads; of these: 992s 18 (100.00%) were unpaired; of these: 992s 15 (83.33%) aligned 0 times 992s 3 (16.67%) aligned exactly 1 time 992s 0 (0.00%) aligned >1 times 992s 16.67% overall alignment rate 992s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 992s Flattened IUPAC characters 992s Mutating sequence Sim.pm.2 992s Introducing 12 SNPs, 0/1 ref/read gaps, and 0 rearrangements 992s Finished SNPs 992s Finished ref gaps 992s Finished read gaps 992s Mutating sequence Sim.pm.1 992s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 992s Finished SNPs 992s Finished ref gaps 992s Finished read gaps 992s Mutated reference genome to subject genome 992s SNPs introduced: 13 992s Reference gaps introduced: 0 992s Read gaps introduced: 1 992s Rearrangements introduced: 0 992s Created read sampler 992s Sampling 121 reads 992s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 992s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 992s parsing sequence Sim.pm.1... 992s parsing sequence Sim.pm.2... 992s Parsed 110 reference bases 992s *** Run 90 of 100 992s /usr/bin/bowtie2 --cp-min 3 --nofw --np 1 --cp-ival 2 --rdg 31.1111553965361 --local --large-index --score-min L,1.03908502139255,9.6384405406506 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 992s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 992s Warning: skipping read '31' because it was < 2 characters long 992s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 992s Warning: skipping read '56' because it was < 2 characters long 992s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 992s Warning: skipping read '102' because it was < 2 characters long 992s 121 reads; of these: 992s 121 (100.00%) were unpaired; of these: 992s 121 (100.00%) aligned 0 times 992s 0 (0.00%) aligned exactly 1 time 992s 0 (0.00%) aligned >1 times 992s 0.00% overall alignment rate 992s Read 50 alignments... 992s Read 100 alignments... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s --- Summary --- 992s Read 1 reference strings 992s Checked 0 alignments, 0 edits 992s --------------- 992s PASSED 992s Flattened IUPAC characters 992s Mutating sequence Sim.pm.1 992s Introducing 15 SNPs, 0/0 ref/read gaps, and 1 rearrangements 992s Finished SNPs 992s Finished ref gaps 992s Finished read gaps 992s Mutating sequence Sim.pm.2 992s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 992s Finished SNPs 992s Finished ref gaps 992s Finished read gaps 992s Mutated reference genome to subject genome 992s SNPs introduced: 20 992s Reference gaps introduced: 0 992s Read gaps introduced: 0 992s Rearrangements introduced: 1 992s Created read sampler 992s Sampling 39 reads 992s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 992s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 992s *** Run 91 of 100 992s /usr/bin/bowtie2 --np 2 -R 1 -D 29 --rfg 47.0668705891278 --trim5 6 --gbar 1 --score-min L,8.0982495696988,7.58775125395454 --cp-min 4 --cp-ival 2 --local --trim3 8 --mp 6.4303396039544,1.17337757848999 -k 8 --large-index -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 992s parsing sequence Sim.pm.1... 992s parsing sequence Sim.pm.2... 992s Parsed 110 reference bases 992s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '4' because it was < 2 characters long 992s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '5' because it was < 2 characters long 992s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '7' because it was < 2 characters long 992s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '8' because it was < 2 characters long 992s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '9' because it was < 2 characters long 992s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '11' because it was < 2 characters long 992s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '12' because it was < 2 characters long 992s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 992s Warning: skipping read '13' because it was < 2 characters long 992s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '14' because it was < 2 characters long 992s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '16' because it was < 2 characters long 992s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '17' because it was < 2 characters long 992s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '26' because it was < 2 characters long 992s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '27' because it was < 2 characters long 992s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '28' because it was < 2 characters long 992s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '33' because it was < 2 characters long 992s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '35' because it was < 2 characters long 992s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '37' because it was < 2 characters long 992s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 992s Warning: skipping read '38' because it was < 2 characters long 992s 39 reads; of these: 992s 39 (100.00%) were unpaired; of these: 992s 39 (100.00%) aligned 0 times 992s 0 (0.00%) aligned exactly 1 time 992s 0 (0.00%) aligned >1 times 992s 0.00% overall alignment rate 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s Processing line... 992s --- Summary --- 992s Read 1 reference strings 992s Checked 0 alignments, 0 edits 992s --------------- 992s PASSED 992s ALSO checking that bowtie2 and bowtie2-align match up 992s /usr/bin/bowtie2 --np 2 -R 1 -D 29 --rfg 47.0668705891278 --trim5 6 --gbar 1 --score-min L,8.0982495696988,7.58775125395454 --cp-min 4 --cp-ival 2 --local --trim3 8 --mp 6.4303396039544,1.17337757848999 -k 8 --large-index -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 993s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '4' because it was < 2 characters long 993s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '5' because it was < 2 characters long 993s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '7' because it was < 2 characters long 993s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '8' because it was < 2 characters long 993s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '9' because it was < 2 characters long 993s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '11' because it was < 2 characters long 993s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '12' because it was < 2 characters long 993s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 993s Warning: skipping read '13' because it was < 2 characters long 993s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '14' because it was < 2 characters long 993s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '16' because it was < 2 characters long 993s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '17' because it was < 2 characters long 993s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '26' because it was < 2 characters long 993s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '27' because it was < 2 characters long 993s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '28' because it was < 2 characters long 993s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '33' because it was < 2 characters long 993s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '35' because it was < 2 characters long 993s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '37' because it was < 2 characters long 993s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '38' because it was < 2 characters long 993s 39 reads; of these: 993s 39 (100.00%) were unpaired; of these: 993s 39 (100.00%) aligned 0 times 993s 0 (0.00%) aligned exactly 1 time 993s 0 (0.00%) aligned >1 times 993s 0.00% overall alignment rate 993s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 993s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 993s /usr/bin/bowtie2 --np 2 -R 1 -D 29 --rfg 47.0668705891278 --trim5 6 --gbar 1 --score-min L,8.0982495696988,7.58775125395454 --cp-min 4 --cp-ival 2 --local --trim3 8 --mp 6.4303396039544,1.17337757848999 -k 8 --large-index -r -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 993s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '4' because it was < 2 characters long 993s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '5' because it was < 2 characters long 993s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '7' because it was < 2 characters long 993s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '8' because it was < 2 characters long 993s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '9' because it was < 2 characters long 993s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '11' because it was < 2 characters long 993s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '12' because it was < 2 characters long 993s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 993s Warning: skipping read '13' because it was < 2 characters long 993s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '14' because it was < 2 characters long 993s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '16' because it was < 2 characters long 993s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '17' because it was < 2 characters long 993s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '26' because it was < 2 characters long 993s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '27' because it was < 2 characters long 993s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '28' because it was < 2 characters long 993s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '33' because it was < 2 characters long 993s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '35' because it was < 2 characters long 993s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '37' because it was < 2 characters long 993s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 993s Warning: skipping read '38' because it was < 2 characters long 993s 39 reads; of these: 993s 39 (100.00%) were unpaired; of these: 993s 39 (100.00%) aligned 0 times 993s 0 (0.00%) aligned exactly 1 time 993s 0 (0.00%) aligned >1 times 993s 0.00% overall alignment rate 993s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 993s Flattened IUPAC characters 993s Mutating sequence Sim.pm.2 993s Introducing 11 SNPs, 1/1 ref/read gaps, and 2 rearrangements 993s Finished SNPs 993s Finished ref gaps 993s Finished read gaps 993s Mutating sequence Sim.pm.1 993s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 993s Finished SNPs 993s Finished ref gaps 993s Finished read gaps 993s Mutated reference genome to subject genome 993s SNPs introduced: 16 993s Reference gaps introduced: 2 993s Read gaps introduced: 1 993s Rearrangements introduced: 2 993s Created read sampler 993s Sampling 119 reads 993s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 993s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 993s parsing sequence Sim.pm.1... 993s *** Run 92 of 100 993s /usr/bin/bowtie2 --norc -R 1 --score-min L,6.58973519090912,7.5789953163893 --gbar 2 --cp-min 3 --cp-ival 1 --mm --mp 7.84415087837392,3.26629213738946 --rdg 46.0404384557331 --local -M 4 --large-index -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 993s parsing sequence Sim.pm.2... 993s Parsed 110 reference bases 993s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 993s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 993s Warning: skipping mate #2 of read '19' because it was < 2 characters long 993s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 993s Warning: skipping mate #1 of read '21' because it was < 2 characters long 993s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 993s Warning: skipping mate #2 of read '29' because it was < 2 characters long 993s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 993s Warning: skipping mate #1 of read '56' because it was < 2 characters long 993s Read 50 alignments... 993s Warning: skipping mate #1 of read '73' because length (1) <= # seed mismatches (0) 993s Warning: skipping mate #1 of read '73' because it was < 2 characters long 993s Read 100 alignments... 993s Read 150 alignments... 993s 119 reads; of these: 993s 119 (100.00%) were paired; of these: 993s 119 (100.00%) aligned concordantly 0 times 993s 0 (0.00%) aligned concordantly exactly 1 time 993s 0 (0.00%) aligned concordantly >1 times 993s ---- 993s 119 pairs aligned concordantly 0 times; of these: 993s 0 (0.00%) aligned discordantly 1 time 993s ---- 993s 119 pairs aligned 0 times concordantly or discordantly; of these: 993s 238 mates make up the pairs; of these: 993s 238 (100.00%) aligned 0 times 993s 0 (0.00%) aligned exactly 1 time 993s 0 (0.00%) aligned >1 times 993s 0.00% overall alignment rate 993s Read 200 alignments... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s Processing line... 993s --- Summary --- 993s Read 1 reference strings 993s Checked 0 alignments, 0 edits 993s --------------- 993s PASSED 993s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 993s /usr/bin/bowtie2 --norc -R 1 --score-min L,6.58973519090912,7.5789953163893 --gbar 2 --cp-min 3 --cp-ival 1 --mm --mp 7.84415087837392,3.26629213738946 --rdg 46.0404384557331 --local -M 4 --large-index -q -p 3 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 993s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 993s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 993s Warning: skipping mate #2 of read '19' because it was < 2 characters long 993s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 993s Warning: skipping mate #1 of read '21' because it was < 2 characters long 993s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 993s Warning: skipping mate #2 of read '29' because it was < 2 characters long 993s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 993s Warning: skipping mate #1 of read '56' because it was < 2 characters long 993s Warning: skipping mate #1 of read '73' because length (1) <= # seed mismatches (0) 993s Warning: skipping mate #1 of read '73' because it was < 2 characters long 993s 119 reads; of these: 993s 119 (100.00%) were paired; of these: 993s 119 (100.00%) aligned concordantly 0 times 993s 0 (0.00%) aligned concordantly exactly 1 time 993s 0 (0.00%) aligned concordantly >1 times 993s ---- 993s 119 pairs aligned concordantly 0 times; of these: 993s 0 (0.00%) aligned discordantly 1 time 993s ---- 993s 119 pairs aligned 0 times concordantly or discordantly; of these: 993s 238 mates make up the pairs; of these: 993s 238 (100.00%) aligned 0 times 993s 0 (0.00%) aligned exactly 1 time 993s 0 (0.00%) aligned >1 times 993s 0.00% overall alignment rate 993s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 993s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 993s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 993s /usr/bin/bowtie2 --norc -R 1 --score-min L,6.58973519090912,7.5789953163893 --gbar 2 --cp-min 3 --cp-ival 1 --mm --mp 7.84415087837392,3.26629213738946 --rdg 46.0404384557331 --local -M 4 --large-index -q -p 3 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 993s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 994s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 994s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 994s Warning: skipping mate #2 of read '19' because it was < 2 characters long 994s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 994s Warning: skipping mate #1 of read '21' because it was < 2 characters long 994s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 994s Warning: skipping mate #2 of read '29' because it was < 2 characters long 994s Warning: skipping mate #1 of read '73' because length (1) <= # seed mismatches (0) 994s Warning: skipping mate #1 of read '73' because it was < 2 characters long 994s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 994s Warning: skipping mate #1 of read '56' because it was < 2 characters long 994s 119 reads; of these: 994s 119 (100.00%) were paired; of these: 994s 119 (100.00%) aligned concordantly 0 times 994s 0 (0.00%) aligned concordantly exactly 1 time 994s 0 (0.00%) aligned concordantly >1 times 994s ---- 994s 119 pairs aligned concordantly 0 times; of these: 994s 0 (0.00%) aligned discordantly 1 time 994s ---- 994s 119 pairs aligned 0 times concordantly or discordantly; of these: 994s 238 mates make up the pairs; of these: 994s 238 (100.00%) aligned 0 times 994s 0 (0.00%) aligned exactly 1 time 994s 0 (0.00%) aligned >1 times 994s 0.00% overall alignment rate 994s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 994s Flattened IUPAC characters 994s Mutating sequence Sim.pm.2 994s Introducing 19 SNPs, 0/0 ref/read gaps, and 1 rearrangements 994s Finished SNPs 994s Finished ref gaps 994s Finished read gaps 994s Mutating sequence Sim.pm.1 994s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 994s Finished SNPs 994s Finished ref gaps 994s Finished read gaps 994s Mutated reference genome to subject genome 994s SNPs introduced: 21 994s Reference gaps introduced: 0 994s Read gaps introduced: 0 994s Rearrangements introduced: 1 994s Created read sampler 994s Sampling 134 reads 994s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 994s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 994s parsing sequence Sim.pm.1... 994s parsing sequence Sim.pm.2... 994s Parsed 110 reference bases 994s *** Run 93 of 100 994s /usr/bin/bowtie2 --cp-min 7 --cp-ival 3 --local --large-index --nofw -D 17 --trim5 2 --gbar 1 --score-min L,3.37256424253246,5.52726018606551 --n-ceil 0.302287043162807,1.22512044298241 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 994s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 994s Warning: skipping read '9' because it was < 2 characters long 994s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 994s Warning: skipping read '13' because it was < 2 characters long 994s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 994s Warning: skipping read '23' because it was < 2 characters long 994s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 994s Warning: skipping read '47' because it was < 2 characters long 994s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 994s Warning: skipping read '70' because it was < 2 characters long 994s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 994s Warning: skipping read '77' because it was < 2 characters long 994s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 994s Warning: skipping read '90' because it was < 2 characters long 994s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 994s Warning: skipping read '99' because it was < 2 characters long 994s Read 50 alignments... 994s Read 100 alignments... 994s 134 reads; of these: 994s 134 (100.00%) were unpaired; of these: 994s 134 (100.00%) aligned 0 times 994s 0 (0.00%) aligned exactly 1 time 994s 0 (0.00%) aligned >1 times 994s 0.00% overall alignment rate 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s --- Summary --- 994s Read 1 reference strings 994s Checked 0 alignments, 0 edits 994s --------------- 994s PASSED 994s Flattened IUPAC characters 994s Mutating sequence Sim.pm.1 994s Introducing 1 SNPs, 0/0 ref/read gaps, and 2 rearrangements 994s Finished SNPs 994s Finished ref gaps 994s Finished read gaps 994s Mutating sequence Sim.pm.2 994s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 994s Finished SNPs 994s Finished ref gaps 994s Finished read gaps 994s Mutated reference genome to subject genome 994s SNPs introduced: 7 994s Reference gaps introduced: 0 994s Read gaps introduced: 1 994s Rearrangements introduced: 3 994s Created read sampler 994s Sampling 74 reads 994s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 994s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 994s parsing sequence Sim.pm.1... 994s *** Run 94 of 100 994s /usr/bin/bowtie2 --rdg 3.86547206601367,17.7008050361501 --large-index -k 12 --cp-min 7 --cp-ival 1 --trim5 1 --rfg 26.1720027460811,4.77803698560835 --score-min L,1.3596127496879,8.81078368235222 --np 1 --qseq -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq 994s parsing sequence Sim.pm.2... 994s Parsed 110 reference bases 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 994s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 994s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 994s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 994s 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 994s 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 994s 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 994s 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 994s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 994s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 994s 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 994s 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 994s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 994s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s Read 50 alignments... 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 994s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 994s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 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 994s 74 reads; of these: 994s 69 (93.24%) were paired; of these: 994s 69 (100.00%) aligned concordantly 0 times 994s 0 (0.00%) aligned concordantly exactly 1 time 994s 0 (0.00%) aligned concordantly >1 times 994s ---- 994s 69 pairs aligned concordantly 0 times; of these: 994s 0 (0.00%) aligned discordantly 1 time 994s ---- 994s 69 pairs aligned 0 times concordantly or discordantly; of these: 994s 138 mates make up the pairs; of these: 994s 117 (84.78%) aligned 0 times 994s 17 (12.32%) aligned exactly 1 time 994s 4 (2.90%) aligned >1 times 994s 5 (6.76%) were unpaired; of these: 994s 5 (100.00%) aligned 0 times 994s 0 (0.00%) aligned exactly 1 time 994s 0 (0.00%) aligned >1 times 994s 14.69% overall alignment rate 994s Read 100 alignments... 994s Read 150 alignments... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s AAAGGG 994s AAAGGG 994s Processing line... 994s Processing line... 994s GACAGG 994s GACAGG 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s CAGGGACGCACAGCATAGTGCGACCGCG 994s CAGGGACGCACAGCATAGTGCGACCGCG 994s Processing line... 994s Processing line... 994s AAG 994s AAG 994s Processing line... 994s AAG 994s AAG 994s Processing line... 994s AAG 994s AAG 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s AGGCGAA 994s AGGCGAA 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s GCCTCGCAGCG 994s GCCTCGCAGCG 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s GCCTCGCAGCGGAAG 994s GCCTCGCAGCGGAAG 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s AG 994s AG 994s Processing line... 994s AG 994s AG 994s Processing line... 994s AG 994s AG 994s Processing line... 994s AG 994s AG 994s Processing line... 994s AG 994s AG 994s Processing line... 994s AG 994s AG 994s Processing line... 994s AG 994s AG 994s Processing line... 994s CT 994s CT 994s Processing line... 994s AG 994s AG 994s Processing line... 994s AG 994s AG 994s Processing line... 994s CT 994s CT 994s Processing line... 994s AG 994s AG 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s AGATGGGACAGGGGAGGCGAACAAAGGGC 994s AGATGGGACAGGGGAGGCGAACAAAGGGC 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s GGGAGGCGAACAAAGGGCCTCGCAG 994s GGGAGGCGAACAAAGGGCCTCGCAG 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s AGGGGAGGCGAACAAAGGGCCTCGCA 994s AGGGGAGGCGAACAAAGGGCCTCGCA 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s ATA 994s ATA 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s GGAGGCGAAC 994s GGAGGCGAAC 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s CAAAGGGCCTCGCAGCGG 994s CAAAGGGCCTCGCAGCGG 994s Processing line... 994s Processing line... 994s GAAGC 994s GAAGC 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s CTC 994s CTC 994s /usr/bin/bowtie2 --rdg 3.86547206601367,17.7008050361501 --large-index -k 12 --cp-min 7 --cp-ival 1 --trim5 1 --rfg 26.1720027460811,4.77803698560835 --score-min L,1.3596127496879,8.81078368235222 --np 1 --qseq -p 2 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.qseq -2 /tmp/Sim.pm.5TNUEKCv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 994s Processing line... 994s CTC 994s CTC 994s Processing line... 994s GAG 994s GAG 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s CGAATGCAGAT 994s CGAATGCAGAT 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s GGAGGCGAACAAAGGGCCTCGCA 994s GGAGGCGAACAAAGGGCCTCGCA 994s Processing line... 994s GGG 994s GGG 994s Processing line... 994s GGG 994s GGG 994s Processing line... 994s GGG 994s GGG 994s Processing line... 994s GGG 994s GGG 994s Processing line... 994s GGG 994s GGG 994s Processing line... 994s GGG 994s GGG 994s Processing line... 994s GGG 994s GGG 994s Processing line... 994s GGG 994s GGG 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s GGGGAGGC 994s GGGGAGGC 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s Processing line... 994s AAAGGGCCTC 994s AAAGGGCCTC 994s Processing line... 994s --- Summary --- 994s Read 1 reference strings 994s Checked 43 alignments, 0 edits 994s --------------- 994s PASSED 994s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 995s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 995s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 995s 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 995s 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 995s 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 995s 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 995s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 995s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 995s 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 995s 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 995s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 995s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 995s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 995s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s 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 995s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 995s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 995s 74 reads; of these: 995s 69 (93.24%) were paired; of these: 995s 69 (100.00%) aligned concordantly 0 times 995s 0 (0.00%) aligned concordantly exactly 1 time 995s 0 (0.00%) aligned concordantly >1 times 995s ---- 995s 69 pairs aligned concordantly 0 times; of these: 995s 0 (0.00%) aligned discordantly 1 time 995s ---- 995s 69 pairs aligned 0 times concordantly or discordantly; of these: 995s 138 mates make up the pairs; of these: 995s 117 (84.78%) aligned 0 times 995s 17 (12.32%) aligned exactly 1 time 995s 4 (2.90%) aligned >1 times 995s 5 (6.76%) were unpaired; of these: 995s 5 (100.00%) aligned 0 times 995s 0 (0.00%) aligned exactly 1 time 995s 0 (0.00%) aligned >1 times 995s 14.69% overall alignment rate 995s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 995s Flattened IUPAC characters 995s Mutating sequence Sim.pm.1 995s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 995s Finished SNPs 995s Finished ref gaps 995s Finished read gaps 995s Mutating sequence Sim.pm.2 995s Introducing 19 SNPs, 0/0 ref/read gaps, and 0 rearrangements 995s Finished SNPs 995s Finished ref gaps 995s Finished read gaps 995s Mutated reference genome to subject genome 995s SNPs introduced: 25 995s Reference gaps introduced: 0 995s Read gaps introduced: 1 995s Rearrangements introduced: 0 995s Created read sampler 995s Sampling 28 reads 995s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fasta & /tmp/Sim.pm.5TNUEKCv_2.fasta 995s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 995s parsing sequence Sim.pm.1... 995s parsing sequence Sim.pm.2... 995s *** Run 95 of 100 995s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 4 --large-index --ma 19.9300747630449 --rdg 48.0447654266865,15.1034164991185 --mp 7.30942139322908,1.60815774681671 -a --np 1 --nofw --score-min L,4.02729568831629,6.26930912253041 --rfg 38.3804227562323,13.0495464495437 -f -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta 995s Parsed 110 reference bases 995s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 995s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 995s Warning: skipping mate #1 of read '7' because it was < 2 characters long 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 995s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 4 --large-index --ma 19.9300747630449 --rdg 48.0447654266865,15.1034164991185 --mp 7.30942139322908,1.60815774681671 -a --np 1 --nofw --score-min L,4.02729568831629,6.26930912253041 --rfg 38.3804227562323,13.0495464495437 -f -p 4 -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 995s 28 reads; of these: 995s 28 (100.00%) were paired; of these: 995s 28 (100.00%) aligned concordantly 0 times 995s 0 (0.00%) aligned concordantly exactly 1 time 995s 0 (0.00%) aligned concordantly >1 times 995s ---- 995s 28 pairs aligned concordantly 0 times; of these: 995s 0 (0.00%) aligned discordantly 1 time 995s ---- 995s 28 pairs aligned 0 times concordantly or discordantly; of these: 995s 56 mates make up the pairs; of these: 995s 51 (91.07%) aligned 0 times 995s 4 (7.14%) aligned exactly 1 time 995s 1 (1.79%) aligned >1 times 995s 8.93% overall alignment rate 995s Read 50 alignments... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s GCAGATGGGACAGGGGAGGCGAACAAAGGGCCTC 995s GCAGATGGGACAGGGGAGGCGAACAAAGGGCCTC 995s Processing line... 995s Processing line... 995s GAATGCAGATGGGACAGGGGAGGCGAACAAAGG 995s GAATGCAGATGGGACAGGGGAGGCGAACAAAGG 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s TCGCAGCGG 995s TCGCAGCGG 995s Processing line... 995s Processing line... 995s GCACAGCAT 995s GCACAGCAT 995s Processing line... 995s Processing line... 995s GGC 995s GGC 995s Processing line... 995s GGC 995s GGC 995s Processing line... 995s GGC 995s GGC 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s Processing line... 995s --- Summary --- 995s Read 1 reference strings 995s Checked 7 alignments, 0 edits 995s --------------- 995s PASSED 995s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 995s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 995s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 995s Warning: skipping mate #1 of read '7' because it was < 2 characters long 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 995s 28 reads; of these: 995s 28 (100.00%) were paired; of these: 995s 28 (100.00%) aligned concordantly 0 times 995s 0 (0.00%) aligned concordantly exactly 1 time 995s 0 (0.00%) aligned concordantly >1 times 995s ---- 995s 28 pairs aligned concordantly 0 times; of these: 995s 0 (0.00%) aligned discordantly 1 time 995s ---- 995s 28 pairs aligned 0 times concordantly or discordantly; of these: 995s 56 mates make up the pairs; of these: 995s 51 (91.07%) aligned 0 times 995s 4 (7.14%) aligned exactly 1 time 995s 1 (1.79%) aligned >1 times 995s 8.93% overall alignment rate 995s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 995s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 995s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 995s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 995s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 4 --large-index --ma 19.9300747630449 --rdg 48.0447654266865,15.1034164991185 --mp 7.30942139322908,1.60815774681671 -a --np 1 --nofw --score-min L,4.02729568831629,6.26930912253041 --rfg 38.3804227562323,13.0495464495437 -f -p 4 -x /tmp/Sim.pm.5TNUEKCv --reorder -1 /tmp/Sim.pm.5TNUEKCv_1.fasta -2 /tmp/Sim.pm.5TNUEKCv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 995s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 995s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 995s Warning: skipping mate #1 of read '7' because it was < 2 characters long 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 995s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 995s 28 reads; of these: 995s 28 (100.00%) were paired; of these: 995s 28 (100.00%) aligned concordantly 0 times 995s 0 (0.00%) aligned concordantly exactly 1 time 995s 0 (0.00%) aligned concordantly >1 times 995s ---- 995s 28 pairs aligned concordantly 0 times; of these: 995s 0 (0.00%) aligned discordantly 1 time 995s ---- 995s 28 pairs aligned 0 times concordantly or discordantly; of these: 995s 56 mates make up the pairs; of these: 995s 51 (91.07%) aligned 0 times 995s 4 (7.14%) aligned exactly 1 time 995s 1 (1.79%) aligned >1 times 995s 8.93% overall alignment rate 995s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 995s Flattened IUPAC characters 995s Mutating sequence Sim.pm.2 995s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 995s Finished SNPs 995s Finished ref gaps 995s Finished read gaps 995s Mutating sequence Sim.pm.1 995s Introducing 10 SNPs, 0/1 ref/read gaps, and 0 rearrangements 995s Finished SNPs 995s Finished ref gaps 995s Finished read gaps 995s Mutated reference genome to subject genome 995s SNPs introduced: 14 995s Reference gaps introduced: 0 995s Read gaps introduced: 1 995s Rearrangements introduced: 0 995s Created read sampler 995s Sampling 207 reads 995s *** Run 96 of 100 995s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 14 --large-index -k 8 --trim3 7 --mp 6.3461450680263,2.33696501918231 --local --np 1 --norc --n-ceil 1.44543158000414,0.464568979799917 --score-min L,3.57536821156102,9.14831597525946 --qseq -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.qseq 995s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.qseq & /tmp/Sim.pm.5TNUEKCv_2.qseq 995s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 995s parsing sequence Sim.pm.1... 995s parsing sequence Sim.pm.2... 995s Parsed 110 reference bases 996s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_139_139_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_144_144_1/1' because length (1) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_151_151_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_155_155_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_155_155_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_160_160_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_160_160_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_161_161_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_164_164_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_164_164_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_167_167_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_167_167_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_172_172_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_172_172_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_177_177_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_177_177_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_179_179_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_179_179_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_182_182_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_182_182_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_183_183_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_183_183_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_185_185_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_185_185_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_195_195_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_195_195_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_197_197_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_197_197_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_198_198_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_198_198_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_201_201_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_201_201_1/1' because it was < 2 characters long 996s Warning: skipping read 'R_1_1_1_204_204_1/1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read 'R_1_1_1_204_204_1/1' because it was < 2 characters long 996s Read 50 alignments... 996s Read 100 alignments... 996s 207 reads; of these: 996s 207 (100.00%) were unpaired; of these: 996s 207 (100.00%) aligned 0 times 996s 0 (0.00%) aligned exactly 1 time 996s 0 (0.00%) aligned >1 times 996s 0.00% overall alignment rate 996s Read 150 alignments... 996s Read 200 alignments... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s --- Summary --- 996s Read 1 reference strings 996s Checked 0 alignments, 0 edits 996s --------------- 996s PASSED 996s Flattened IUPAC characters 996s Mutating sequence Sim.pm.2 996s Introducing 6 SNPs, 1/0 ref/read gaps, and 2 rearrangements 996s Finished SNPs 996s Finished ref gaps 996s Finished read gaps 996s Mutating sequence Sim.pm.1 996s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 996s Finished SNPs 996s Finished ref gaps 996s Finished read gaps 996s Mutated reference genome to subject genome 996s SNPs introduced: 11 996s Reference gaps introduced: 1 996s Read gaps introduced: 0 996s Rearrangements introduced: 2 996s Created read sampler 996s Sampling 56 reads 996s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 996s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 996s *** Run 97 of 100 996s /usr/bin/bowtie2 --large-index --n-ceil 0.00811076987973202,1.08544039994592 --score-min L,5.75614852983161,9.56688446513619 --rdg 14.3262987540734 -a --mm --cp-ival 1 --cp-min 12 --np 4 -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 996s parsing sequence Sim.pm.1... 996s parsing sequence Sim.pm.2... 996s Parsed 110 reference bases 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 996s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #1 of read '2' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 996s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #2 of read '11' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 996s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #1 of read '17' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 996s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #1 of read '24' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 996s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #2 of read '32' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 996s Read 50 alignments... 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 996s Read 100 alignments... 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 996s 56 reads; of these: 996s 56 (100.00%) were paired; of these: 996s 56 (100.00%) aligned concordantly 0 times 996s 0 (0.00%) aligned concordantly exactly 1 time 996s 0 (0.00%) aligned concordantly >1 times 996s ---- 996s 56 pairs aligned concordantly 0 times; of these: 996s 0 (0.00%) aligned discordantly 1 time 996s ---- 996s 56 pairs aligned 0 times concordantly or discordantly; of these: 996s 112 mates make up the pairs; of these: 996s 90 (80.36%) aligned 0 times 996s 17 (15.18%) aligned exactly 1 time 996s 5 (4.46%) aligned >1 times 996s 19.64% overall alignment rate 996s Read 150 alignments... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s ATGGGACAGGGGAGGCGAACAA 996s ATGGGACAGGGGAGGCGAACAA 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GGGACGCACAGCATAGTG 996s GGGACGCACAGCATAGTG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GACAGGGGAGGC 996s GACAGGGGAGGC 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s CAGCG 996s CAGCG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GGGGAGGCGAACAAAGGGCCTC 996s GGGGAGGCGAACAAAGGGCCTC 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GAGGCGAACAAAGGGCCTCGC 996s GAGGCGAACAAAGGGCCTCGC 996s Processing line... 996s Processing line... 996s GAACAAAG 996s GAACAAAG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s ATGGGACAGGGGAGGCGAACAAAGGG 996s ATGGGACAGGGGAGGCGAACAAAGGG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s AAAGGGCCTC 996s AAAGGGCCTC 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GGGAC 996s GGGAC 996s Processing line... 996s GGGAC 996s GGGAC 996s Processing line... 996s Processing line... 996s GGGCCTCGCAGCG 996s GGGCCTCGCAGCG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s TGGGACAGGGGAGGCGAACAAAGGGCCT 996s TGGGACAGGGGAGGCGAACAAAGGGCCT 996s Processing line... 996s Processing line... 996s AC 996s AC 996s Processing line... 996s AC 996s AC 996s Processing line... 996s AC 996s AC 996s Processing line... 996s GT 996s GT 996s Processing line... 996s GT 996s GT 996s Processing line... 996s AC 996s AC 996s Processing line... 996s AC 996s AC 996s Processing line... 996s GT 996s GT 996s Processing line... 996s Processing line... 996s AAGGGCCT 996s AAGGGCCT 996s Processing line... 996s Processing line... 996s GACAGGGGAGGCGAACA 996s GACAGGGGAGGCGAACA 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s ACAAAGGGCCTCGC 996s ACAAAGGGCCTCGC 996s Processing line... 996s Processing line... 996s CA 996s CA 996s Processing line... 996s CA 996s CA 996s Processing line... 996s TG 996s TG 996s Processing line... 996s CA 996s CA 996s Processing line... 996s CA 996s CA 996s Processing line... 996s CA 996s CA 996s Processing line... 996s CA 996s CA 996s Processing line... 996s TG 996s TG 996s Processing line... 996s CA 996s CA 996s Processing line... 996s TG 996s TG 996s Processing line... 996s CA 996s CA 996s Processing line... 996s TG 996s TG 996s Processing line... 996s CA 996s CA 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s AAT 996s AAT 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s AGGGGA 996s AGGGGA 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s TCCAGG 996s TCCAGG 996s Processing line... 996s Processing line... 996s AG 996s AG 996s Processing line... 996s AG 996s AG 996s Processing line... 996s AG 996s AG 996s Processing line... 996s CT 996s CT 996s Processing line... 996s AG 996s AG 996s Processing line... 996s AG 996s AG 996s Processing line... 996s CT 996s CT 996s Processing line... 996s AG 996s AG 996s Processing line... 996s AG 996s AG 996s Processing line... 996s AG 996s AG 996s Processing line... 996s AG 996s AG 996s Processing line... 996s CT 996s CT 996s Processing line... 996s AG 996s AG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GGGA 996s GGGA 996s Processing line... 996s GGGA 996s GGGA 996s Processing line... 996s GGGA 996s GGGA 996s Processing line... 996s GGGA 996s GGGA 996s Processing line... 996s Processing line... 996s Processing line... 996s --- Summary --- 996s Read 1 reference strings 996s Checked 57 alignments, 0 edits 996s --------------- 996s PASSED 996s Flattened IUPAC characters 996s Mutating sequence Sim.pm.1 996s Introducing 6 SNPs, 2/1 ref/read gaps, and 0 rearrangements 996s Finished SNPs 996s Finished ref gaps 996s Finished read gaps 996s Mutating sequence Sim.pm.2 996s Introducing 2 SNPs, 0/0 ref/read gaps, and 3 rearrangements 996s Finished SNPs 996s Finished ref gaps 996s Finished read gaps 996s Mutated reference genome to subject genome 996s SNPs introduced: 8 996s Reference gaps introduced: 2 996s Read gaps introduced: 1 996s Rearrangements introduced: 3 996s Created read sampler 996s Sampling 86 reads 996s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 996s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 996s parsing sequence Sim.pm.1... 996s parsing sequence Sim.pm.2... 996s Parsed 110 reference bases 996s *** Run 98 of 100 996s /usr/bin/bowtie2 --rfg 46.4983790076162,7.9468648277612 -i S,2.34445366835155 --mp 9.50777390280775,8.2048946779296 --trim5 0 --score-min L,5.55252830170324,3.95141332683625 --large-index --n-ceil 0.325552431480939,0.770476929140528 --nofw --np 2 --cp-min 5 --cp-ival 1 -q -x /tmp/Sim.pm.5TNUEKCv -1 /tmp/Sim.pm.5TNUEKCv_1.fastq -2 /tmp/Sim.pm.5TNUEKCv_2.fastq 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 996s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #1 of read '7' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 996s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #2 of read '19' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 996s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #1 of read '25' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 996s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #1 of read '44' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 996s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #1 of read '52' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 996s Read 50 alignments... 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 996s Read 100 alignments... 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 996s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 996s Warning: skipping mate #2 of read '80' because it was < 2 characters long 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 996s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 996s 86 reads; of these: 996s 86 (100.00%) were paired; of these: 996s 86 (100.00%) aligned concordantly 0 times 996s 0 (0.00%) aligned concordantly exactly 1 time 996s 0 (0.00%) aligned concordantly >1 times 996s ---- 996s 86 pairs aligned concordantly 0 times; of these: 996s 0 (0.00%) aligned discordantly 1 time 996s ---- 996s 86 pairs aligned 0 times concordantly or discordantly; of these: 996s 172 mates make up the pairs; of these: 996s 156 (90.70%) aligned 0 times 996s 12 (6.98%) aligned exactly 1 time 996s 4 (2.33%) aligned >1 times 996s 9.30% overall alignment rate 996s Read 150 alignments... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GGAA 996s GGAA 996s Processing line... 996s Processing line... 996s ATGGGACAGGGGAGGCGAACAAAGGGCCT 996s ATGGGACAGGGGAGGCGAACAAAGGGCCT 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GGCCTCGCAGCGG 996s GGCCTCGCAGCGG 996s Processing line... 996s Processing line... 996s AATGCAG 996s AATGCAG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s AAAGGGCC 996s AAAGGGCC 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s CTCGCAGCGG 996s CTCGCAGCGG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s TAGTGCGACCGCG 996s TAGTGCGACCGCG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GCAGAT 996s GCAGAT 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s CTCGCAGC 996s CTCGCAGC 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GCC 996s GCC 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s TG 996s TG 996s Processing line... 996s Processing line... 996s GA 996s GA 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s TAGTGCGAC 996s TAGTGCGAC 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GGGAGGCGA 996s GGGAGGCGA 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s CG 996s CG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s GCCTCG 996s GCCTCG 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s --- Summary --- 996s Read 1 reference strings 996s Checked 16 alignments, 0 edits 996s --------------- 996s PASSED 996s Flattened IUPAC characters 996s Mutating sequence Sim.pm.2 996s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 996s Finished SNPs 996s Finished ref gaps 996s Finished read gaps 996s Mutating sequence Sim.pm.1 996s Introducing 2 SNPs, 2/1 ref/read gaps, and 0 rearrangements 996s Finished SNPs 996s Finished ref gaps 996s Finished read gaps 996s Mutated reference genome to subject genome 996s SNPs introduced: 11 996s Reference gaps introduced: 2 996s Read gaps introduced: 1 996s Rearrangements introduced: 0 996s Created read sampler 996s Sampling 36 reads 996s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.fastq & /tmp/Sim.pm.5TNUEKCv_2.fastq 996s *** Run 99 of 100 996s /usr/bin/bowtie2 --cp-min 2 --np 14 -N 0 -L28 --mm --cp-ival 1 --trim5 5 --rdg 27.2664997659868 --mp 8.03510876604554,6.24638766746174 -a --local --rfg 10.5854494198054 --large-index --score-min L,3.13920663009983,3.2870262593018 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq 996s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 996s parsing sequence Sim.pm.1... 996s parsing sequence Sim.pm.2... 996s Parsed 110 reference bases 996s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 996s Warning: skipping read '1' because it was < 2 characters long 996s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 996s Warning: skipping read '3' because it was < 2 characters long 996s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 996s Warning: skipping read '5' because it was < 2 characters long 996s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 996s Warning: skipping read '28' because it was < 2 characters long 996s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 996s Warning: skipping read '33' because it was < 2 characters long 996s 36 reads; of these: 996s 36 (100.00%) were unpaired; of these: 996s 36 (100.00%) aligned 0 times 996s 0 (0.00%) aligned exactly 1 time 996s 0 (0.00%) aligned >1 times 996s 0.00% overall alignment rate 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s /usr/bin/bowtie2 --cp-min 2 --np 14 -N 0 -L28 --mm --cp-ival 1 --trim5 5 --rdg 27.2664997659868 --mp 8.03510876604554,6.24638766746174 -a --local --rfg 10.5854494198054 --large-index --score-min L,3.13920663009983,3.2870262593018 -q -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.als 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s Processing line... 996s --- Summary --- 996s Read 1 reference strings 996s Checked 0 alignments, 0 edits 996s --------------- 996s PASSED 996s ALSO checking that bowtie2 and bowtie2-align match up 997s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '1' because it was < 2 characters long 997s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '3' because it was < 2 characters long 997s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '5' because it was < 2 characters long 997s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '28' because it was < 2 characters long 997s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '33' because it was < 2 characters long 997s 36 reads; of these: 997s 36 (100.00%) were unpaired; of these: 997s 36 (100.00%) aligned 0 times 997s 0 (0.00%) aligned exactly 1 time 997s 0 (0.00%) aligned >1 times 997s 0.00% overall alignment rate 997s diff -uw /tmp/Sim.pm.5TNUEKCv.als /tmp/Sim.pm.5TNUEKCv.debug.als 997s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 997s /usr/bin/bowtie2 --cp-min 2 --np 14 -N 0 -L28 --mm --cp-ival 1 --trim5 5 --rdg 27.2664997659868 --mp 8.03510876604554,6.24638766746174 -a --local --rfg 10.5854494198054 --large-index --score-min L,3.13920663009983,3.2870262593018 -q -p 3 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 997s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '1' because it was < 2 characters long 997s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '3' because it was < 2 characters long 997s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '5' because it was < 2 characters long 997s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '28' because it was < 2 characters long 997s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '33' because it was < 2 characters long 997s 36 reads; of these: 997s 36 (100.00%) were unpaired; of these: 997s 36 (100.00%) aligned 0 times 997s 0 (0.00%) aligned exactly 1 time 997s 0 (0.00%) aligned >1 times 997s 0.00% overall alignment rate 997s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 997s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 997s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 997s /usr/bin/bowtie2 --cp-min 2 --np 14 -N 0 -L28 --mm --cp-ival 1 --trim5 5 --rdg 27.2664997659868 --mp 8.03510876604554,6.24638766746174 -a --local --rfg 10.5854494198054 --large-index --score-min L,3.13920663009983,3.2870262593018 -q -p 4 -x /tmp/Sim.pm.5TNUEKCv --reorder /tmp/Sim.pm.5TNUEKCv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.reord.als 997s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 997s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '1' because it was < 2 characters long 997s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '3' because it was < 2 characters long 997s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '5' because it was < 2 characters long 997s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '28' because it was < 2 characters long 997s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '33' because it was < 2 characters long 997s 36 reads; of these: 997s 36 (100.00%) were unpaired; of these: 997s 36 (100.00%) aligned 0 times 997s 0 (0.00%) aligned exactly 1 time 997s 0 (0.00%) aligned >1 times 997s 0.00% overall alignment rate 997s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als /tmp/Sim.pm.5TNUEKCv.px.reord.als 997s Flattened IUPAC characters 997s Mutating sequence Sim.pm.1 997s Introducing 10 SNPs, 1/0 ref/read gaps, and 0 rearrangements 997s Finished SNPs 997s Finished ref gaps 997s Finished read gaps 997s Mutating sequence Sim.pm.2 997s Introducing 7 SNPs, 0/2 ref/read gaps, and 0 rearrangements 997s Finished SNPs 997s Finished ref gaps 997s Finished read gaps 997s Mutated reference genome to subject genome 997s SNPs introduced: 17 997s Reference gaps introduced: 1 997s Read gaps introduced: 2 997s Rearrangements introduced: 0 997s Created read sampler 997s Sampling 34 reads 997s Dumping reads to temporary files /tmp/Sim.pm.5TNUEKCv_1.raw & /tmp/Sim.pm.5TNUEKCv_2.raw 997s Parsing FASTA file /tmp/Sim.pm.5TNUEKCv.fa... 997s parsing sequence Sim.pm.1... 997s parsing sequence Sim.pm.2... 997s Parsed 110 reference bases 997s *** Run 100 of 100 997s /usr/bin/bowtie2 -N 0 -L16 --nofw --np 4 --gbar 2 --score-min L,3.23741368445575,9.11880249674349 --mm --cp-ival 4 --cp-min 6 --large-index --ma 4.37969153666579 --trim3 7 -a -r -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw 997s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 997s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 997s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '1' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 997s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '2' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 997s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '3' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 997s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '7' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 997s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '11' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 997s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '22' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 997s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '24' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 997s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '32' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 997s 34 reads; of these: 997s 34 (100.00%) were unpaired; of these: 997s 30 (88.24%) aligned 0 times 997s 2 (5.88%) aligned exactly 1 time 997s 2 (5.88%) aligned >1 times 997s 11.76% overall alignment rate 997s Read 50 alignments... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s TGCGACCGC 997s TGCGACCGC 997s Processing line... 997s AGGCGAACAAAGGGCCTCGCAGCGG 997s AGGCGAACAAAGGGCCTCGCAGCGG 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s AG 997s AG 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s Processing line... 997s --- Summary --- 997s Read 1 reference strings 997s Checked 22 alignments, 0 edits 997s --------------- 997s PASSED 997s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 997s /usr/bin/bowtie2 -N 0 -L16 --nofw --np 4 --gbar 2 --score-min L,3.23741368445575,9.11880249674349 --mm --cp-ival 4 --cp-min 6 --large-index --ma 4.37969153666579 --trim3 7 -a -r -p 3 -x /tmp/Sim.pm.5TNUEKCv /tmp/Sim.pm.5TNUEKCv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als 997s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 997s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 997s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '1' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 997s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '2' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 997s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '3' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 997s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '7' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 997s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '11' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 997s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '22' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 997s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '24' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 997s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 997s Warning: skipping read '32' because it was < 2 characters long 997s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 997s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 997s 34 reads; of these: 997s 34 (100.00%) were unpaired; of these: 997s 30 (88.24%) aligned 0 times 997s 2 (5.88%) aligned exactly 1 time 997s 2 (5.88%) aligned >1 times 997s 11.76% overall alignment rate 997s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.px.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.px.als.sorted 997s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.5TNUEKCv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.5TNUEKCv.debug.als.sorted 998s diff -uw /tmp/Sim.pm.5TNUEKCv.debug.als.sorted /tmp/Sim.pm.5TNUEKCv.px.als.sorted 998s Created DNA generator 998s N frac: 0.035 998s IUPAC frac: 0.002 998s AT/ACGT frac: 0.428 998s A/AT frac: 0.629 998s C/CG frac: 0.345 998s Generating 2 references 998s Generated reference 'Sim.pm.1' of untrimmed length 122, trimmed length 21 998s Generated reference 'Sim.pm.2' of untrimmed length 163, trimmed length 60 998s Wrote references to /tmp/Sim.pm.rtAHg7h8.fa 998s A: 18 998s C: 22 998s G: 22 998s N: 4 998s T: 15 998s Executing: /usr/bin/bowtie2-build --threads 1 --bmax 8824 --large-index --dcv 16 --offrate 2 /tmp/Sim.pm.rtAHg7h8.fa /tmp/Sim.pm.rtAHg7h8 998s *** TEST CASE *** 998s Building a LARGE indexSettings: 998s Output files: "/tmp/Sim.pm.rtAHg7h8.*.bt2l" 998s Line rate: 7 (line is 128 bytes) 998s Lines per side: 1 (side is 128 bytes) 998s Offset rate: 2 (one in 4) 998s FTable chars: 10 998s Strings: unpacked 998s Max bucket size: 8824 998s Max bucket size, sqrt multiplier: default 998s Max bucket size, len divisor: default 998s Difference-cover sample period: 16 998s Endianness: little 998s Actual local endianness: little 998s Sanity checking: disabled 998s Assertions: disabled 998s Random seed: 0 998s Sizeofs: void*:8, int:4, long:8, size_t:8 998s Input files DNA, FASTA: 998s /tmp/Sim.pm.rtAHg7h8.fa 998s Reading reference sizes 998s 998s Time reading reference sizes: 00:00:00 998s Calculating joined length 998s Writing header 998s Reserving space for joined string 998s Joining reference sequences 998s Time to join reference sequences: 00:00:00 998s bmax according to bmax setting: 8824 998s Using parameters --bmax 6618 --dcv 16 998s Doing ahead-of-time memory usage test 998s Passed! Constructing with these parameters: --bmax 6618 --dcv 16 998s Constructing suffix-array element generator 998s Building DifferenceCoverSample 998s Building sPrime 998s Building sPrimeOrder 998s V-Sorting samples 998s V-Sorting samples time: 00:00:00 998s Allocating rank array 998s Ranking v-sort output 998s Ranking v-sort output time: 00:00:00 998s Invoking Larsson-Sadakane on ranks 998s Invoking Larsson-Sadakane on ranks time: 00:00:00 998s Sanity-checking and returning 998s Skipping building samples since text length 77 is less than bucket size: 6618 998s Converting suffix-array elements to index image 998s Allocating ftab, absorbFtab 998s Entering Ebwt loop 998s Getting block 1 of 1 998s No samples; assembling all-inclusive block 998s Sorting block of length 77 for bucket 1 998s (Using difference cover) 998s Sorting block time: 00:00:00 998s Returning block of 78 for bucket 1 998s Exited Ebwt loop 998s fchr[A]: 0 998s fchr[C]: 18 998s fchr[G]: 40 998s fchr[T]: 62 998s fchr[$]: 77 998s Exiting Ebwt::buildToDisk() 998s Returning from initFromVector 998s Wrote 8389131 bytes to primary EBWT file: /tmp/Sim.pm.rtAHg7h8.1.bt2l.tmp 998s Wrote 164 bytes to secondary EBWT file: /tmp/Sim.pm.rtAHg7h8.2.bt2l.tmp 998s Re-opening _in1 and _in2 as input streams 998s Returning from Ebwt constructor 998s Headers: 998s len: 77 998s bwtLen: 78 998s sz: 20 998s bwtSz: 20 998s lineRate: 7 998s offRate: 2 998s offMask: 0xfffffffffffffffc 998s ftabChars: 10 998s eftabLen: 20 998s eftabSz: 160 998s ftabLen: 1048577 998s ftabSz: 8388616 998s offsLen: 20 998s offsSz: 160 998s lineSz: 128 998s sideSz: 128 998s sideBwtSz: 96 998s sideBwtLen: 384 998s numSides: 1 998s numLines: 1 998s ebwtTotLen: 128 998s ebwtTotSz: 128 998s color: 0 998s reverse: 0 998s Total time for call to driver() for forward index: 00:00:00 998s Reading reference sizes 998s Time reading reference sizes: 00:00:00 998s Calculating joined length 998s Writing header 998s Reserving space for joined string 998s Joining reference sequences 998s Time to join reference sequences: 00:00:00 998s Time to reverse reference sequence: 00:00:00 998s bmax according to bmax setting: 8824 998s Using parameters --bmax 6618 --dcv 16 998s Doing ahead-of-time memory usage test 998s Passed! Constructing with these parameters: --bmax 6618 --dcv 16 998s Constructing suffix-array element generator 998s Building DifferenceCoverSample 998s Building sPrime 998s Building sPrimeOrder 998s V-Sorting samples 998s V-Sorting samples time: 00:00:00 998s Allocating rank array 998s Ranking v-sort output 998s Ranking v-sort output time: 00:00:00 998s Invoking Larsson-Sadakane on ranks 998s Invoking Larsson-Sadakane on ranks time: 00:00:00 998s Sanity-checking and returning 998s Skipping building samples since text length 77 is less than bucket size: 6618 998s Converting suffix-array elements to index image 998s Allocating ftab, absorbFtab 998s Entering Ebwt loop 998s Getting block 1 of 1 998s No samples; assembling all-inclusive block 998s Sorting block of length 77 for bucket 1 998s (Using difference cover) 998s Sorting block time: 00:00:00 998s Returning block of 78 for bucket 1 998s Exited Ebwt loop 998s fchr[A]: 0 998s fchr[C]: 18 998s fchr[G]: 40 998s fchr[T]: 62 998s fchr[$]: 77 998s Exiting Ebwt::buildToDisk() 998s Returning from initFromVector 998s Wrote 8389131 bytes to primary EBWT file: /tmp/Sim.pm.rtAHg7h8.rev.1.bt2l.tmp 998s Wrote 164 bytes to secondary EBWT file: /tmp/Sim.pm.rtAHg7h8.rev.2.bt2l.tmp 998s Re-opening _in1 and _in2 as input streams 998s Renaming Returning from Ebwt constructor 998s Headers: 998s len: 77 998s bwtLen: 78 998s sz: 20 998s bwtSz: 20 998s lineRate: 7 998s offRate: 2 998s offMask: 0xfffffffffffffffc 998s ftabChars: 10 998s eftabLen: 20 998s eftabSz: 160 998s ftabLen: 1048577 998s ftabSz: 8388616 998s offsLen: 20 998s offsSz: 160 998s lineSz: 128 998s sideSz: 128 998s sideBwtSz: 96 998s sideBwtLen: 384 998s numSides: 1 998s numLines: 1 998s ebwtTotLen: 128 998s ebwtTotSz: 128 998s color: 0 998s reverse: 1 998s Total time for backward call to driver() for mirror index: 00:00:00 998s /tmp/Sim.pm.rtAHg7h8.3.bt2l.tmp to /tmp/Sim.pm.rtAHg7h8.3.bt2l 998s Renaming /tmp/Sim.pm.rtAHg7h8.4.bt2l.tmp to /tmp/Sim.pm.rtAHg7h8.4.bt2l 998s Renaming /tmp/Sim.pm.rtAHg7h8.1.bt2l.tmp to /tmp/Sim.pm.rtAHg7h8.1.bt2l 998s Renaming /tmp/Sim.pm.rtAHg7h8.2.bt2l.tmp to /tmp/Sim.pm.rtAHg7h8.2.bt2l 998s Renaming /tmp/Sim.pm.rtAHg7h8.rev.1.bt2l.tmp to /tmp/Sim.pm.rtAHg7h8.rev.1.bt2l 998s Renaming /tmp/Sim.pm.rtAHg7h8.rev.2.bt2l.tmp to /tmp/Sim.pm.rtAHg7h8.rev.2.bt2l 998s Built nucleotide index '/tmp/Sim.pm.rtAHg7h8' 998s Flattened IUPAC characters 998s Mutating sequence Sim.pm.1 998s Introducing 3 SNPs, 0/2 ref/read gaps, and 0 rearrangements 998s Finished SNPs 998s Finished ref gaps 998s Finished read gaps 998s Mutating sequence Sim.pm.2 998s Introducing 11 SNPs, 1/1 ref/read gaps, and 0 rearrangements 998s Finished SNPs 998s Finished ref gaps 998s Finished read gaps 998s Mutated reference genome to subject genome 998s SNPs introduced: 14 998s Reference gaps introduced: 1 998s Read gaps introduced: 3 998s Rearrangements introduced: 0 998s Created read sampler 998s *** Run 1 of 100 998s /usr/bin/bowtie2 --cp-ival 1 --cp-min 2 --large-index --score-min L,7.14537377858384,5.97438031007644 --trim3 5 --mp 9.04903708499305,7.75005365570754 --rdg 4.28861126235312,9.92219726526494 --local -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta 998s Sampling 9 reads 998s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 998s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 998s parsing sequence Sim.pm.1... 998s parsing sequence Sim.pm.2... 998s Parsed 81 reference bases 999s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 999s Warning: skipping read '2' because it was < 2 characters long 999s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 999s Warning: skipping read '3' because it was < 2 characters long 999s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 999s Warning: skipping read '7' because it was < 2 characters long 999s 9 reads; of these: 999s 9 (100.00%) were unpaired; of these: 999s 9 (100.00%) aligned 0 times 999s 0 (0.00%) aligned exactly 1 time 999s 0 (0.00%) aligned >1 times 999s 0.00% overall alignment rate 999s /usr/bin/bowtie2 --cp-ival 1 --cp-min 2 --large-index --score-min L,7.14537377858384,5.97438031007644 --trim3 5 --mp 9.04903708499305,7.75005365570754 --rdg 4.28861126235312,9.92219726526494 --local -f -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s --- Summary --- 999s Read 1 reference strings 999s Checked 0 alignments, 0 edits 999s --------------- 999s PASSED 999s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 999s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 999s Warning: skipping read '2' because it was < 2 characters long 999s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 999s Warning: skipping read '3' because it was < 2 characters long 999s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 999s Warning: skipping read '7' because it was < 2 characters long 999s 9 reads; of these: 999s 9 (100.00%) were unpaired; of these: 999s 9 (100.00%) aligned 0 times 999s 0 (0.00%) aligned exactly 1 time 999s 0 (0.00%) aligned >1 times 999s 0.00% overall alignment rate 999s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 999s Flattened IUPAC characters 999s Mutating sequence Sim.pm.1 999s Introducing 4 SNPs, 3/1 ref/read gaps, and 1 rearrangements 999s Finished SNPs 999s Finished ref gaps 999s Finished read gaps 999s Mutating sequence Sim.pm.2 999s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 999s Finished SNPs 999s Finished ref gaps 999s Finished read gaps 999s Mutated reference genome to subject genome 999s SNPs introduced: 6 999s Reference gaps introduced: 3 999s Read gaps introduced: 1 999s Rearrangements introduced: 1 999s Created read sampler 999s Sampling 95 reads 999s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 999s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 999s parsing sequence Sim.pm.1... 999s parsing sequence Sim.pm.2... 999s Parsed 81 reference bases 999s *** Run 2 of 100 999s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 2 --large-index --ma 9.25081563569574 --trim3 3 --mp 9.73224106907868,3.08354442897312 -a --norc --n-ceil 0.872927102120036,0.707439959110877 --score-min L,4.65423563383987,3.49448904117177 --trim5 1 -i S,0.438980185107009 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 999s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 999s 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 999s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 999s 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 999s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 999s 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 999s 95 reads; of these: 999s 95 (100.00%) were unpaired; of these: 999s 87 (91.58%) aligned 0 times 999s 5 (5.26%) aligned exactly 1 time 999s 3 (3.16%) aligned >1 times 999s 8.42% overall alignment rate 999s Read 50 alignments... 999s Read 100 alignments... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s TA 999s TA 999s Processing line... 999s TA 999s TA 999s Processing line... 999s TA 999s TA 999s Processing line... 999s TA 999s TA 999s Processing line... 999s TA 999s TA 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s AT 999s AT 999s Processing line... 999s AT 999s AT 999s Processing line... 999s AT 999s AT 999s Processing line... 999s AT 999s AT 999s Processing line... 999s AT 999s AT 999s Processing line... 999s Processing line... 999s Processing line... 999s TTCACG 999s TTCACG 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s TGGGCGAC 999s TGGGCGAC 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s AACCGAAAGACGGAC 999s AACCGAAAGACGGAC 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s ATGACAAC 999s ATGACAAC 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s TGGGCGA 999s TGGGCGA 999s Processing line... 999s Processing line... 999s Processing line... 999s TG 999s TG 999s Processing line... 999s TG 999s TG 999s Processing line... 999s TG 999s TG 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s Processing line... 999s --- Summary --- 999s Read 1 reference strings 999s Checked 18 alignments, 0 edits 999s --------------- 999s PASSED 999s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 999s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 2 --large-index --ma 9.25081563569574 --trim3 3 --mp 9.73224106907868,3.08354442897312 -a --norc --n-ceil 0.872927102120036,0.707439959110877 --score-min L,4.65423563383987,3.49448904117177 --trim5 1 -i S,0.438980185107009 --qseq -p 3 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 999s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 999s 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 999s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 999s 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 999s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 999s 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 999s 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 999s 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 999s 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 999s 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 999s 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 999s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 999s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 999s 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 999s 95 reads; of these: 999s 95 (100.00%) were unpaired; of these: 999s 87 (91.58%) aligned 0 times 999s 5 (5.26%) aligned exactly 1 time 999s 3 (3.16%) aligned >1 times 999s 8.42% overall alignment rate 999s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 999s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 999s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 999s Flattened IUPAC characters 999s Mutating sequence Sim.pm.2 999s Introducing 13 SNPs, 1/0 ref/read gaps, and 0 rearrangements 999s Finished SNPs 999s Finished ref gaps 999s Finished read gaps 999s Mutating sequence Sim.pm.1 999s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 999s Finished SNPs 999s Finished ref gaps 999s Finished read gaps 999s Mutated reference genome to subject genome 999s SNPs introduced: 19 999s Reference gaps introduced: 1 999s Read gaps introduced: 0 999s Rearrangements introduced: 0 999s Created read sampler 999s Sampling 86 reads 999s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 999s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 999s parsing sequence Sim.pm.1... 999s parsing sequence Sim.pm.2... 999s *** Run 3 of 100 999s /usr/bin/bowtie2 -D 32 --norc --gbar 3 --score-min L,1.37295410814746,6.66962660426193 --trim5 2 --mm --cp-ival 1 --cp-min 5 --large-index --mp 6.16790474498268,5.03797814027785 -a --trim3 7 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 999s Parsed 81 reference bases 999s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 999s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 999s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 999s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 999s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 999s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 999s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 999s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 999s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 999s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 999s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1000s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1000s Warning: skipping read '8' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1000s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1000s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1000s Warning: skipping read '25' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1000s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1000s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1000s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 1000s Warning: skipping mate #2 of read '30' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1000s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1000s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1000s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (0) 1000s Warning: skipping mate #2 of read '47' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1000s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '49' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1000s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1000s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1000s Read 50 alignments... 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1000s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1000s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1000s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '74' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1000s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 1000s Warning: skipping read '76' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1000s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read '80' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1000s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 1000s Warning: skipping read '82' because it was < 2 characters long 1000s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1000s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1000s Read 100 alignments... 1000s 86 reads; of these: 1000s 70 (81.40%) were paired; of these: 1000s 69 (98.57%) aligned concordantly 0 times 1000s 0 (0.00%) aligned concordantly exactly 1 time 1000s 1 (1.43%) aligned concordantly >1 times 1000s ---- 1000s 69 pairs aligned concordantly 0 times; of these: 1000s 0 (0.00%) aligned discordantly 1 time 1000s ---- 1000s 69 pairs aligned 0 times concordantly or discordantly; of these: 1000s 138 mates make up the pairs; of these: 1000s 128 (92.75%) aligned 0 times 1000s 5 (3.62%) aligned exactly 1 time 1000s 5 (3.62%) aligned >1 times 1000s 16 (18.60%) were unpaired; of these: 1000s 15 (93.75%) aligned 0 times 1000s 1 (6.25%) aligned exactly 1 time 1000s 0 (0.00%) aligned >1 times 1000s 8.33% overall alignment rate 1000s Read 150 alignments... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s TATCGCGT 1000s TATCGCGT 1000s Processing line... 1000s TCCCGTATCGCGTAG 1000s TCCCGTATCGCGTAG 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s GCGA 1000s GCGA 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s ACAACCGAAAGAC 1000s ACAACCGAAAGAC 1000s Processing line... 1000s Processing line... 1000s ACG 1000s ACG 1000s Processing line... 1000s ACG 1000s ACG 1000s Processing line... 1000s ACG 1000s ACG 1000s Processing line... 1000s ACG 1000s ACG 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s AT 1000s AT 1000s Processing line... 1000s AT 1000s AT 1000s Processing line... 1000s AT 1000s AT 1000s Processing line... 1000s AT 1000s AT 1000s Processing line... 1000s AT 1000s AT 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s GACA 1000s GACA 1000s Processing line... 1000s Processing line... 1000s TCGCGTA 1000s TCGCGTA 1000s Processing line... 1000s TCGCGTA 1000s TCGCGTA 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s CGC 1000s CGC 1000s Processing line... 1000s CGC 1000s CGC 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s AAA 1000s AAA 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s ACA 1000s ACA 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s AC 1000s AC 1000s Processing line... 1000s AC 1000s AC 1000s Processing line... 1000s AC 1000s AC 1000s Processing line... 1000s AC 1000s AC 1000s Processing line... 1000s AC 1000s AC 1000s Processing line... 1000s AC 1000s AC 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s AACC 1000s AACC 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s --- Summary --- 1000s Read 1 reference strings 1000s Checked 27 alignments, 0 edits 1000s --------------- 1000s PASSED 1000s Flattened IUPAC characters 1000s Mutating sequence Sim.pm.1 1000s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1000s Finished SNPs 1000s Finished ref gaps 1000s Finished read gaps 1000s Mutating sequence Sim.pm.2 1000s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1000s Finished SNPs 1000s Finished ref gaps 1000s Finished read gaps 1000s Mutated reference genome to subject genome 1000s SNPs introduced: 3 1000s Reference gaps introduced: 0 1000s Read gaps introduced: 1 1000s Rearrangements introduced: 0 1000s Created read sampler 1000s Sampling 114 reads 1000s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1000s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1000s parsing sequence Sim.pm.1... 1000s parsing sequence Sim.pm.2... 1000s Parsed 81 reference bases 1000s *** Run 4 of 100 1000s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 2 --large-index --mp 5.75868559791161,1.78326931902109 --local -N 1 -L14 -D 43 --score-min L,9.56048887997938,7.70761398698538 --rfg 6.83771596066927 --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq 1000s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1000s Warning: skipping mate #2 of read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #2 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1000s Read 50 alignments... 1000s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1000s Read 100 alignments... 1000s Read 150 alignments... 1000s 114 reads; of these: 1000s 114 (100.00%) were paired; of these: 1000s 114 (100.00%) aligned concordantly 0 times 1000s 0 (0.00%) aligned concordantly exactly 1 time 1000s 0 (0.00%) aligned concordantly >1 times 1000s ---- 1000s 114 pairs aligned concordantly 0 times; of these: 1000s 0 (0.00%) aligned discordantly 1 time 1000s ---- 1000s 114 pairs aligned 0 times concordantly or discordantly; of these: 1000s 228 mates make up the pairs; of these: 1000s 228 (100.00%) aligned 0 times 1000s 0 (0.00%) aligned exactly 1 time 1000s 0 (0.00%) aligned >1 times 1000s 0.00% overall alignment rate 1000s Read 200 alignments... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s --- Summary --- 1000s Read 1 reference strings 1000s Checked 0 alignments, 0 edits 1000s --------------- 1000s PASSED 1000s ALSO checking that bowtie2 and bowtie2-align match up 1000s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 2 --large-index --mp 5.75868559791161,1.78326931902109 --local -N 1 -L14 -D 43 --score-min L,9.56048887997938,7.70761398698538 --rfg 6.83771596066927 --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1000s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1000s Warning: skipping mate #2 of read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #2 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (1) 1000s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1000s 114 reads; of these: 1000s 114 (100.00%) were paired; of these: 1000s 114 (100.00%) aligned concordantly 0 times 1000s 0 (0.00%) aligned concordantly exactly 1 time 1000s 0 (0.00%) aligned concordantly >1 times 1000s ---- 1000s 114 pairs aligned concordantly 0 times; of these: 1000s 0 (0.00%) aligned discordantly 1 time 1000s ---- 1000s 114 pairs aligned 0 times concordantly or discordantly; of these: 1000s 228 mates make up the pairs; of these: 1000s 228 (100.00%) aligned 0 times 1000s 0 (0.00%) aligned exactly 1 time 1000s 0 (0.00%) aligned >1 times 1000s 0.00% overall alignment rate 1000s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1000s Flattened IUPAC characters 1000s Mutating sequence Sim.pm.2 1000s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1000s Finished SNPs 1000s Finished ref gaps 1000s Finished read gaps 1000s Mutating sequence Sim.pm.1 1000s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1000s Finished SNPs 1000s Finished ref gaps 1000s Finished read gaps 1000s Mutated reference genome to subject genome 1000s SNPs introduced: 6 1000s Reference gaps introduced: 0 1000s Read gaps introduced: 1 1000s Rearrangements introduced: 2 1000s Created read sampler 1000s Sampling 92 reads 1000s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1000s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1000s parsing sequence Sim.pm.1... 1000s parsing sequence Sim.pm.2... 1000s *** Run 5 of 100 1000s /usr/bin/bowtie2 --trim3 1 --mp 7.62356426939506,3.16104167312781 --local --large-index -M 4 --cp-min 2 --cp-ival 2 --trim5 1 --score-min L,2.43735851821279,6.7449698794272 -R 1 --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq 1000s Parsed 81 reference bases 1000s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1000s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1000s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1000s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1000s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 1000s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1000s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1000s Read 50 alignments... 1000s Read 100 alignments... 1000s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 1000s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1000s 92 reads; of these: 1000s 84 (91.30%) were paired; of these: 1000s 84 (100.00%) aligned concordantly 0 times 1000s 0 (0.00%) aligned concordantly exactly 1 time 1000s 0 (0.00%) aligned concordantly >1 times 1000s ---- 1000s 84 pairs aligned concordantly 0 times; of these: 1000s 0 (0.00%) aligned discordantly 1 time 1000s ---- 1000s 84 pairs aligned 0 times concordantly or discordantly; of these: 1000s 168 mates make up the pairs; of these: 1000s 168 (100.00%) aligned 0 times 1000s 0 (0.00%) aligned exactly 1 time 1000s 0 (0.00%) aligned >1 times 1000s 8 (8.70%) were unpaired; of these: 1000s 8 (100.00%) aligned 0 times 1000s 0 (0.00%) aligned exactly 1 time 1000s 0 (0.00%) aligned >1 times 1000s 0.00% overall alignment rate 1000s Read 150 alignments... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s Processing line... 1000s --- Summary --- 1000s /usr/bin/bowtie2 --trim3 1 --mp 7.62356426939506,3.16104167312781 --local --large-index -M 4 --cp-min 2 --cp-ival 2 --trim5 1 --score-min L,2.43735851821279,6.7449698794272 -R 1 --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1000s Read 1 reference strings 1000s Checked 0 alignments, 0 edits 1000s --------------- 1000s PASSED 1000s ALSO checking that bowtie2 and bowtie2-align match up 1001s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1001s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1001s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1001s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1001s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1001s 92 reads; of these: 1001s 84 (91.30%) were paired; of these: 1001s 84 (100.00%) aligned concordantly 0 times 1001s 0 (0.00%) aligned concordantly exactly 1 time 1001s 0 (0.00%) aligned concordantly >1 times 1001s ---- 1001s 84 pairs aligned concordantly 0 times; of these: 1001s 0 (0.00%) aligned discordantly 1 time 1001s ---- 1001s 84 pairs aligned 0 times concordantly or discordantly; of these: 1001s 168 mates make up the pairs; of these: 1001s 168 (100.00%) aligned 0 times 1001s 0 (0.00%) aligned exactly 1 time 1001s 0 (0.00%) aligned >1 times 1001s 8 (8.70%) were unpaired; of these: 1001s 8 (100.00%) aligned 0 times 1001s 0 (0.00%) aligned exactly 1 time 1001s 0 (0.00%) aligned >1 times 1001s 0.00% overall alignment rate 1001s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1001s /usr/bin/bowtie2 --trim3 1 --mp 7.62356426939506,3.16104167312781 --local --large-index -M 4 --cp-min 2 --cp-ival 2 --trim5 1 --score-min L,2.43735851821279,6.7449698794272 -R 1 --qseq -p 4 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1001s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1001s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1001s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1001s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1001s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1001s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1001s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1001s 92 reads; of these: 1001s 84 (91.30%) were paired; of these: 1001s 84 (100.00%) aligned concordantly 0 times 1001s 0 (0.00%) aligned concordantly exactly 1 time 1001s 0 (0.00%) aligned concordantly >1 times 1001s ---- 1001s 84 pairs aligned concordantly 0 times; of these: 1001s 0 (0.00%) aligned discordantly 1 time 1001s ---- 1001s 84 pairs aligned 0 times concordantly or discordantly; of these: 1001s 168 mates make up the pairs; of these: 1001s 168 (100.00%) aligned 0 times 1001s 0 (0.00%) aligned exactly 1 time 1001s 0 (0.00%) aligned >1 times 1001s 8 (8.70%) were unpaired; of these: 1001s 8 (100.00%) aligned 0 times 1001s 0 (0.00%) aligned exactly 1 time 1001s 0 (0.00%) aligned >1 times 1001s 0.00% overall alignment rate 1001s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1001s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1001s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1001s Flattened IUPAC characters 1001s Mutating sequence Sim.pm.2 1001s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1001s Finished SNPs 1001s Finished ref gaps 1001s Finished read gaps 1001s Mutating sequence Sim.pm.1 1001s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1001s Finished SNPs 1001s Finished ref gaps 1001s Finished read gaps 1001s Mutated reference genome to subject genome 1001s SNPs introduced: 5 1001s Reference gaps introduced: 0 1001s Read gaps introduced: 1 1001s Rearrangements introduced: 0 1001s Created read sampler 1001s Sampling 134 reads 1001s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1001s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1001s parsing sequence Sim.pm.1... 1001s *** Run 6 of 100 1001s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 5 --large-index -M 2 --local -R 1 -D 6 --gbar 1 --score-min L,1.51964352567201,2.80212576136956 --trim5 2 --rfg 32.1294195153754 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1001s parsing sequence Sim.pm.2... 1001s Parsed 81 reference bases 1001s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1001s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1001s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read '25' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '25' because it was < 2 characters long 1001s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1001s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1001s Warning: skipping read '56' because it was < 2 characters long 1001s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 1001s Read 50 alignments... 1001s Warning: skipping read '74' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '76' because it was < 2 characters long 1001s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read '77' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '78' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '78' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '90' because it was < 2 characters long 1001s Read 100 alignments... 1001s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read '108' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '109' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '109' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '134' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '134' because it was < 2 characters long 1001s Read 150 alignments... 1001s Read 200 alignments... 1001s 134 reads; of these: 1001s 128 (95.52%) were paired; of these: 1001s 128 (100.00%) aligned concordantly 0 times 1001s 0 (0.00%) aligned concordantly exactly 1 time 1001s 0 (0.00%) aligned concordantly >1 times 1001s ---- 1001s 128 pairs aligned concordantly 0 times; of these: 1001s 0 (0.00%) aligned discordantly 1 time 1001s ---- 1001s 128 pairs aligned 0 times concordantly or discordantly; of these: 1001s 256 mates make up the pairs; of these: 1001s 256 (100.00%) aligned 0 times 1001s 0 (0.00%) aligned exactly 1 time 1001s 0 (0.00%) aligned >1 times 1001s 6 (4.48%) were unpaired; of these: 1001s 6 (100.00%) aligned 0 times 1001s 0 (0.00%) aligned exactly 1 time 1001s 0 (0.00%) aligned >1 times 1001s 0.00% overall alignment rate 1001s Read 250 alignments... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing 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line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s Processing line... 1001s --- Summary --- 1001s Read 1 reference strings 1001s Checked 0 alignments, 0 edits 1001s --------------- 1001s PASSED 1001s ALSO checking that bowtie2 and bowtie2-align match up 1001s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 5 --large-index -M 2 --local -R 1 -D 6 --gbar 1 --score-min L,1.51964352567201,2.80212576136956 --trim5 2 --rfg 32.1294195153754 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1001s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1001s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1001s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read '25' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '25' because it was < 2 characters long 1001s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1001s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1001s Warning: skipping read '56' because it was < 2 characters long 1001s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 1001s Warning: skipping read '74' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '76' because it was < 2 characters long 1001s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read '77' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '78' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '78' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '90' because it was < 2 characters long 1001s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 1001s Warning: skipping mate #1 of read '108' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '109' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '109' because it was < 2 characters long 1001s Warning: skipping mate #2 of read '134' because length (1) <= # seed mismatches (0) 1001s Warning: skipping mate #2 of read '134' because it was < 2 characters long 1001s 134 reads; of these: 1001s 128 (95.52%) were paired; of these: 1001s 128 (100.00%) aligned concordantly 0 times 1001s 0 (0.00%) aligned concordantly exactly 1 time 1001s 0 (0.00%) aligned concordantly >1 times 1001s ---- 1001s 128 pairs aligned concordantly 0 times; of these: 1001s 0 (0.00%) aligned discordantly 1 time 1001s ---- 1001s 128 pairs aligned 0 times concordantly or discordantly; of these: 1001s 256 mates make up the pairs; of these: 1001s 256 (100.00%) aligned 0 times 1001s 0 (0.00%) aligned exactly 1 time 1001s 0 (0.00%) aligned >1 times 1001s 6 (4.48%) were unpaired; of these: 1001s 6 (100.00%) aligned 0 times 1001s 0 (0.00%) aligned exactly 1 time 1001s 0 (0.00%) aligned >1 times 1001s 0.00% overall alignment rate 1002s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1002s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1002s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 5 --large-index -M 2 --local -R 1 -D 6 --gbar 1 --score-min L,1.51964352567201,2.80212576136956 --trim5 2 --rfg 32.1294195153754 -q -p 4 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1002s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1002s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1002s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1002s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 1002s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1002s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 1002s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 1002s Warning: skipping mate #1 of read '25' because it was < 2 characters long 1002s Warning: skipping mate #2 of read '25' because it was < 2 characters long 1002s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1002s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1002s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1002s Warning: skipping read '56' because it was < 2 characters long 1002s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 1002s Warning: skipping mate #2 of read '90' because it was < 2 characters long 1002s Warning: skipping mate #2 of read '134' because length (1) <= # seed mismatches (0) 1002s Warning: skipping mate #2 of read '134' because it was < 2 characters long 1002s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 1002s Warning: skipping mate #1 of read '108' because it was < 2 characters long 1002s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 1002s Warning: skipping read '74' because it was < 2 characters long 1002s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 1002s Warning: skipping mate #2 of read '76' because it was < 2 characters long 1002s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 1002s Warning: skipping mate #1 of read '77' because it was < 2 characters long 1002s Warning: skipping mate #2 of read '78' because length (1) <= # seed mismatches (0) 1002s Warning: skipping mate #2 of read '78' because it was < 2 characters long 1002s Warning: skipping mate #2 of read '109' because length (1) <= # seed mismatches (0) 1002s Warning: skipping mate #2 of read '109' because it was < 2 characters long 1002s 134 reads; of these: 1002s 128 (95.52%) were paired; of these: 1002s 128 (100.00%) aligned concordantly 0 times 1002s 0 (0.00%) aligned concordantly exactly 1 time 1002s 0 (0.00%) aligned concordantly >1 times 1002s ---- 1002s 128 pairs aligned concordantly 0 times; of these: 1002s 0 (0.00%) aligned discordantly 1 time 1002s ---- 1002s 128 pairs aligned 0 times concordantly or discordantly; of these: 1002s 256 mates make up the pairs; of these: 1002s 256 (100.00%) aligned 0 times 1002s 0 (0.00%) aligned exactly 1 time 1002s 0 (0.00%) aligned >1 times 1002s 6 (4.48%) were unpaired; of these: 1002s 6 (100.00%) aligned 0 times 1002s 0 (0.00%) aligned exactly 1 time 1002s 0 (0.00%) aligned >1 times 1002s 0.00% overall alignment rate 1002s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1002s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1002s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1002s Flattened IUPAC characters 1002s Mutating sequence Sim.pm.2 1002s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1002s Finished SNPs 1002s Finished ref gaps 1002s Finished read gaps 1002s Mutating sequence Sim.pm.1 1002s Introducing 3 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1002s Finished SNPs 1002s Finished ref gaps 1002s Finished read gaps 1002s Mutated reference genome to subject genome 1002s SNPs introduced: 6 1002s Reference gaps introduced: 1 1002s Read gaps introduced: 2 1002s Rearrangements introduced: 0 1002s Created read sampler 1002s Sampling 74 reads 1002s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1002s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1002s parsing sequence Sim.pm.1... 1002s parsing sequence Sim.pm.2... 1002s Parsed 81 reference bases 1002s *** Run 7 of 100 1002s /usr/bin/bowtie2 --large-index -M 3 --score-min L,7.33292139242325,1.99451404508841 --trim3 8 --rfg 19.0570678118853,11.1343166876663 --local --cp-ival 1 -R 1 --cp-min 2 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1002s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1002s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '1' because it was < 2 characters long 1002s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '5' because it was < 2 characters long 1002s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '12' because it was < 2 characters long 1002s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '14' because it was < 2 characters long 1002s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '15' because it was < 2 characters long 1002s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '16' because it was < 2 characters long 1002s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 1002s Warning: skipping read '19' because it was < 2 characters long 1002s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '21' because it was < 2 characters long 1002s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '26' because it was < 2 characters long 1002s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '28' because it was < 2 characters long 1002s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '33' because it was < 2 characters long 1002s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '38' because it was < 2 characters long 1002s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '40' because it was < 2 characters long 1002s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '46' because it was < 2 characters long 1002s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 1002s Warning: skipping read '48' because it was < 2 characters long 1002s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '50' because it was < 2 characters long 1002s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '51' because it was < 2 characters long 1002s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '52' because it was < 2 characters long 1002s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '54' because it was < 2 characters long 1002s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 1002s Warning: skipping read '57' because it was < 2 characters long 1002s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '61' because it was < 2 characters long 1002s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '65' because it was < 2 characters long 1002s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1002s Warning: skipping read '69' because it was < 2 characters long 1002s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '70' because it was < 2 characters long 1002s 74 reads; of these: 1002s 74 (100.00%) were unpaired; of these: 1002s 74 (100.00%) aligned 0 times 1002s 0 (0.00%) aligned exactly 1 time 1002s 0 (0.00%) aligned >1 times 1002s 0.00% overall alignment rate 1002s Read 50 alignments... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s Processing line... 1002s --- Summary --- 1002s Read 1 reference strings 1002s Checked 0 alignments, 0 edits 1002s --------------- 1002s PASSED 1002s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1002s /usr/bin/bowtie2 --large-index -M 3 --score-min L,7.33292139242325,1.99451404508841 --trim3 8 --rfg 19.0570678118853,11.1343166876663 --local --cp-ival 1 -R 1 --cp-min 2 -r -p 3 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1002s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1002s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '1' because it was < 2 characters long 1002s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '5' because it was < 2 characters long 1002s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '12' because it was < 2 characters long 1002s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '14' because it was < 2 characters long 1002s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '15' because it was < 2 characters long 1002s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '16' because it was < 2 characters long 1002s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 1002s Warning: skipping read '19' because it was < 2 characters long 1002s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '21' because it was < 2 characters long 1002s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '26' because it was < 2 characters long 1002s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '28' because it was < 2 characters long 1002s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '33' because it was < 2 characters long 1002s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '38' because it was < 2 characters long 1002s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '40' because it was < 2 characters long 1002s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '46' because it was < 2 characters long 1002s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 1002s Warning: skipping read '48' because it was < 2 characters long 1002s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '50' because it was < 2 characters long 1002s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '51' because it was < 2 characters long 1002s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '52' because it was < 2 characters long 1002s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '54' because it was < 2 characters long 1002s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 1002s Warning: skipping read '57' because it was < 2 characters long 1002s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '61' because it was < 2 characters long 1002s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '65' because it was < 2 characters long 1002s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1002s Warning: skipping read '69' because it was < 2 characters long 1002s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1002s Warning: skipping read '70' because it was < 2 characters long 1002s 74 reads; of these: 1002s 74 (100.00%) were unpaired; of these: 1002s 74 (100.00%) aligned 0 times 1002s 0 (0.00%) aligned exactly 1 time 1002s 0 (0.00%) aligned >1 times 1002s 0.00% overall alignment rate 1002s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1002s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1002s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1002s Flattened IUPAC characters 1002s Mutating sequence Sim.pm.2 1002s Introducing 10 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1002s Finished SNPs 1002s Finished ref gaps 1002s Finished read gaps 1002s Mutating sequence Sim.pm.1 1002s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1002s Finished SNPs 1002s Finished ref gaps 1002s Finished read gaps 1002s Mutated reference genome to subject genome 1002s SNPs introduced: 13 1002s Reference gaps introduced: 0 1002s Read gaps introduced: 0 1002s Rearrangements introduced: 4 1002s Created read sampler 1002s Sampling 107 reads 1002s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1002s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1002s parsing sequence Sim.pm.1... 1002s parsing sequence Sim.pm.2... 1002s Parsed 81 reference bases 1002s *** Run 8 of 100 1002s /usr/bin/bowtie2 --cp-ival 3 --cp-min 2 --large-index --score-min L,7.08257634379854,2.28529078105917 --mp 6.59217657117872,4.80583739583203 --rdg 25.4680158294651,10.3163891373636 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1003s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 1003s Warning: skipping read '37' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1003s Warning: skipping read '73' because length (1) <= # seed mismatches (0) 1003s Warning: skipping read '73' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1003s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 1003s Warning: skipping read '95' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1003s 107 reads; of these: 1003s 107 (100.00%) were unpaired; of these: 1003s 82 (76.64%) aligned 0 times 1003s 15 (14.02%) aligned exactly 1 time 1003s 10 (9.35%) aligned >1 times 1003s 23.36% overall alignment rate 1003s Read 50 alignments... 1003s Read 100 alignments... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s AC 1003s AC 1003s Processing line... 1003s CG 1003s CG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s AAAG 1003s AAAG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s ACGTA 1003s ACGTA 1003s Processing line... 1003s ACGTA 1003s ACGTA 1003s Processing line... 1003s GTTCACG 1003s GTTCACG 1003s Processing line... 1003s GAC 1003s GAC 1003s Processing line... 1003s Processing line... 1003s ATCCCGTATCGCGTA 1003s ATCCCGTATCGCGTA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s ACGT 1003s ACGT 1003s Processing line... 1003s CCTG 1003s CCTG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s AT 1003s AT 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s TTCACGTGGG 1003s TTCACGTGGG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s ATGACAACCGAAAGACGGACGTA 1003s ATGACAACCGAAAGACGGACGTA 1003s Processing line... 1003s Processing line... 1003s AAAG 1003s AAAG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s CTGT 1003s CTGT 1003s Processing line... 1003s ATCCCGTATCGCGTA 1003s ATCCCGTATCGCGTA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s AAAG 1003s AAAG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s GT 1003s GT 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s ACAACCGAAAGA 1003s ACAACCGAAAGA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s CTC 1003s CTC 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s TCA 1003s TCA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s TA 1003s TA 1003s Processing line... 1003s Processing line... 1003s CCGAAAGACGG 1003s CCGAAAGACGG 1003s Processing line... 1003s ACGGACGT 1003s ACGGACGT 1003s Processing line... 1003s ACCGAAAGAC 1003s ACCGAAAGAC 1003s --- Summary --- 1003s Read 1 reference strings 1003s Checked 25 alignments, 0 edits 1003s --------------- 1003s PASSED 1003s Flattened IUPAC characters 1003s Mutating sequence Sim.pm.1 1003s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1003s Finished SNPs 1003s Finished ref gaps 1003s Finished read gaps 1003s Mutating sequence Sim.pm.2 1003s Introducing 14 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1003s Finished SNPs 1003s Finished ref gaps 1003s Finished read gaps 1003s Mutated reference genome to subject genome 1003s SNPs introduced: 17 1003s Reference gaps introduced: 1 1003s Read gaps introduced: 0 1003s Rearrangements introduced: 0 1003s Created read sampler 1003s Sampling 152 reads 1003s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1003s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1003s parsing sequence Sim.pm.1... 1003s parsing sequence Sim.pm.2... 1003s Parsed 81 reference bases 1003s *** Run 9 of 100 1003s /usr/bin/bowtie2 -R 4 -D 13 --np 1 --score-min L,6.56957729133501,6.54414669668883 --rfg 35.1103818031878,8.4819055343801 --trim5 6 --mm --cp-ival 2 --cp-min 2 --large-index --rdg 20.7581350097626 --mp 6.86850036160207,5.35037797446462 --trim3 8 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1003s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '0' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1003s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '1' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1003s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '5' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1003s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '7' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1003s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '8' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1003s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '10' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1003s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 1003s Warning: skipping read '14' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1003s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 1003s Warning: skipping read '18' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1003s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '21' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1003s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '28' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1003s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '29' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1003s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '31' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1003s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '32' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1003s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '35' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1003s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '36' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1003s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '38' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1003s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '40' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1003s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '41' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1003s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '42' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1003s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '44' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1003s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '48' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1003s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '49' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1003s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '51' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1003s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '53' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1003s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '54' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1003s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '57' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1003s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '59' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1003s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '61' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1003s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '62' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1003s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '64' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1003s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '69' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1003s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '70' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1003s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '71' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1003s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '74' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1003s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '77' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1003s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '82' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1003s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '83' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1003s Warning: skipping read '85' because length (1) <= # seed mismatches (0) 1003s Warning: skipping read '85' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1003s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '92' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1003s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '102' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1003s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '113' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1003s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '117' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1003s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '122' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1003s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '123' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1003s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '124' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1003s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '126' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1003s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '127' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1003s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '130' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1003s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '132' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1003s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '134' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 1003s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '138' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 1003s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '140' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 1003s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '142' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 1003s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 1003s Warning: skipping read '144' because it was < 2 characters long 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 1003s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 1003s 152 reads; of these: 1003s 152 (100.00%) were unpaired; of these: 1003s 137 (90.13%) aligned 0 times 1003s 6 (3.95%) aligned exactly 1 time 1003s 9 (5.92%) aligned >1 times 1003s 9.87% overall alignment rate 1003s Read 50 alignments... 1003s Read 100 alignments... 1003s Read 150 alignments... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s GA 1003s GA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s AGA 1003s AGA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s AACCGAAAGAC 1003s AACCGAAAGAC 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s GT 1003s GT 1003s Processing line... 1003s GC 1003s GC 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s GA 1003s GA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s CCGTAT 1003s CCGTAT 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s TAT 1003s TAT 1003s Processing line... 1003s CCTGTTCA 1003s CCTGTTCA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s CG 1003s CG 1003s Processing line... 1003s Processing line... 1003s ACGTG 1003s ACGTG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s CAACCGAAAGA 1003s CAACCGAAAGA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s ACCGA 1003s ACCGA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s CGTG 1003s CGTG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s CACGTGGGC 1003s CACGTGGGC 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s --- Summary --- 1003s Read 1 reference strings 1003s Checked 15 alignments, 0 edits 1003s --------------- 1003s PASSED 1003s Flattened IUPAC characters 1003s Mutating sequence Sim.pm.1 1003s Introducing 0 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1003s Finished SNPs 1003s *** Run 10 of 100 1003s /usr/bin/bowtie2 -N 1 -L18 --mm --cp-ival 1 --cp-min 2 --np 9 --large-index -k 2 --score-min L,9.23178830542695,3.34670247857911 --rdg 24.0537839809301 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1003s Finished ref gaps 1003s Finished read gaps 1003s Mutating sequence Sim.pm.2 1003s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1003s Finished SNPs 1003s Finished ref gaps 1003s Finished read gaps 1003s Mutated reference genome to subject genome 1003s SNPs introduced: 7 1003s Reference gaps introduced: 0 1003s Read gaps introduced: 2 1003s Rearrangements introduced: 1 1003s Created read sampler 1003s Sampling 67 reads 1003s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1003s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1003s parsing sequence Sim.pm.1... 1003s parsing sequence Sim.pm.2... 1003s Parsed 81 reference bases 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (1) 1003s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 67 reads; of these: 1003s 67 (100.00%) were unpaired; of these: 1003s 51 (76.12%) aligned 0 times 1003s 9 (13.43%) aligned exactly 1 time 1003s 7 (10.45%) aligned >1 times 1003s 23.88% overall alignment rate 1003s Read 50 alignments... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s ATCGCGTAG 1003s ATCGCGTAG 1003s Processing line... 1003s ATCGCGTAG 1003s ATCGCGTAG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s TCACGT 1003s TCACGT 1003s Processing line... 1003s Processing line... 1003s TCCTGTTCACGTGGGC 1003s TCCTGTTCACGTGGGC 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s GACGGACGTA 1003s GACGGACGTA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s TCACGT 1003s TCACGT 1003s Processing line... 1003s CG 1003s CG 1003s Processing line... 1003s CG 1003s CG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s CCTGTTCA 1003s CCTGTTCA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s CTGT 1003s CTGT 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s CCGTATC 1003s CCGTATC 1003s Processing line... 1003s CCGTATC 1003s CCGTATC 1003s Processing line... 1003s Processing line... 1003s CCTGTTCA 1003s CCTGTTCA 1003s Processing line... 1003s CCGAAAGACGGACGTA 1003s CCGAAAGACGGACGTA 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s GATGACAACCG 1003s GATGACAACCG 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s Processing line... 1003s GCGT 1003s GCGT 1003s Processing line... 1003s GCGT 1003s GCGT 1003s Processing line... 1003s TG 1003s TG 1003s Processing line... 1003s TG 1003s TG 1003s Processing line... 1003s CGTAG 1003s CGTAG 1003s Processing line... 1003s CGTAG 1003s CGTAG 1003s Processing line... 1003s GAC 1003s GAC 1003s Processing line... 1003s /usr/bin/bowtie2 -N 1 -L18 --mm --cp-ival 1 --cp-min 2 --np 9 --large-index -k 2 --score-min L,9.23178830542695,3.34670247857911 --rdg 24.0537839809301 --qseq -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1003s GAC 1003s GAC 1003s --- Summary --- 1003s Read 1 reference strings 1003s Checked 23 alignments, 0 edits 1003s --------------- 1003s PASSED 1003s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (1) 1003s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 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 1003s 67 reads; of these: 1003s 67 (100.00%) were unpaired; of these: 1003s 51 (76.12%) aligned 0 times 1003s 9 (13.43%) aligned exactly 1 time 1003s 7 (10.45%) aligned >1 times 1003s 23.88% overall alignment rate 1003s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1003s Flattened IUPAC characters 1003s Mutating sequence Sim.pm.1 1003s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1003s Finished SNPs 1003s Finished ref gaps 1003s Finished read gaps 1003s Mutating sequence Sim.pm.2 1003s Introducing 1 SNPs, 0/2 ref/read gaps, and 1 rearrangements 1003s Finished SNPs 1003s Finished ref gaps 1003s Finished read gaps 1003s Mutated reference genome to subject genome 1003s SNPs introduced: 4 1003s Reference gaps introduced: 0 1003s Read gaps introduced: 2 1003s Rearrangements introduced: 2 1003s Created read sampler 1003s Sampling 227 reads 1003s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1003s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1003s parsing sequence Sim.pm.1... 1003s parsing sequence Sim.pm.2... 1003s Parsed 81 reference bases 1003s *** Run 11 of 100 1003s /usr/bin/bowtie2 --trim3 6 --rdg 49.0701905824087 --trim5 7 --score-min L,4.79857853328771,7.02310421129868 --gbar 6 --large-index --np 6 --cp-min 2 --cp-ival 1 --mm -N 1 -L16 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1004s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '1' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1004s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '7' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1004s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '8' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1004s Warning: skipping read '9' because length (1) <= # seed mismatches (1) 1004s Warning: skipping read '9' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1004s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '10' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1004s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '14' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1004s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '19' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1004s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '20' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1004s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '21' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1004s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '25' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1004s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '29' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1004s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '31' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1004s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '33' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1004s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '37' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1004s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '39' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1004s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '40' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1004s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '42' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1004s Warning: skipping read '44' because length (1) <= # seed mismatches (1) 1004s Warning: skipping read '44' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1004s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '45' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1004s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '46' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1004s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '49' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1004s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '52' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1004s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '53' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1004s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '55' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1004s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '58' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1004s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '61' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1004s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '62' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1004s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '65' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1004s Warning: skipping read '66' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '66' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1004s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '67' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1004s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '70' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1004s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '73' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1004s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '75' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1004s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '83' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1004s Warning: skipping read '87' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '87' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1004s Warning: skipping read '89' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '89' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1004s Warning: skipping read '90' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '90' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1004s Warning: skipping read '94' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '94' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1004s Warning: skipping read '95' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '95' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1004s Warning: skipping read '97' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '97' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1004s Warning: skipping read '98' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '98' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1004s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '99' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1004s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '100' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1004s Warning: skipping read '102' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '102' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1004s Warning: skipping read '103' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '103' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1004s Warning: skipping read '104' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '104' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1004s Warning: skipping read '105' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '105' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1004s Warning: skipping read '107' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '107' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1004s Warning: skipping read '109' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '109' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1004s Warning: skipping read '110' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '110' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1004s Warning: skipping read '113' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '113' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1004s Warning: skipping read '114' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '114' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1004s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '119' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1004s Warning: skipping read '123' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '123' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1004s Warning: skipping read '124' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '124' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1004s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '125' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1004s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '126' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1004s Warning: skipping read '129' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '129' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 1004s Warning: skipping read '139' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '139' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 1004s Warning: skipping read '140' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '140' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 1004s Warning: skipping read '141' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '141' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 1004s Warning: skipping read '142' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '142' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 1004s Warning: skipping read '143' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '143' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 1004s Warning: skipping read '145' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '145' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 1004s Warning: skipping read '149' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '149' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 1004s Warning: skipping read '150' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '150' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 1004s Warning: skipping read '151' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '151' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 1004s Warning: skipping read '153' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '153' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 1004s Warning: skipping read '154' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '154' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 1004s Warning: skipping read '158' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '158' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 1004s Warning: skipping read '160' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '160' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 1004s Warning: skipping read '161' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '161' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 1004s Warning: skipping read '163' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '163' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 1004s Warning: skipping read '165' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '165' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 1004s Warning: skipping read '167' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '167' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 1004s Warning: skipping read '172' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '172' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 1004s Warning: skipping read '177' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '177' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 1004s Warning: skipping read '178' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '178' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 1004s Warning: skipping read '179' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '179' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 1004s Warning: skipping read '183' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '183' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '189; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '190; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '191; setting to 0 instead 1004s Warning: skipping read '191' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '191' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '192; setting to 0 instead 1004s Warning: skipping read '192' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '192' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '193; setting to 0 instead 1004s Warning: skipping read '193' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '193' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '194; setting to 0 instead 1004s Warning: skipping read '194' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '194' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '195; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '196; setting to 0 instead 1004s Warning: skipping read '196' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '196' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '197; setting to 0 instead 1004s Warning: skipping read '197' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '197' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '198; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '199; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '200; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '201; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '202; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '203; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '204; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '205; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '206; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '207; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '208; setting to 0 instead 1004s Warning: skipping read '208' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '208' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '209; setting to 0 instead 1004s Read 50 alignments... 1004s Read 100 alignments... 1004s Read 150 alignments... 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '210; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '211; setting to 0 instead 1004s Warning: skipping read '211' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '211' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '212; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '213; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '214; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '215; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '216; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '217; setting to 0 instead 1004s Warning: skipping read '217' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '217' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '218; setting to 0 instead 1004s Warning: skipping read '218' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '218' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '219; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '220; setting to 0 instead 1004s Warning: skipping read '220' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '220' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '221; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '222; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '223; setting to 0 instead 1004s Warning: skipping read '223' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '223' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '224; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '225; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '226; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '227; setting to 0 instead 1004s Read 200 alignments... 1004s 227 reads; of these: 1004s 227 (100.00%) were unpaired; of these: 1004s 207 (91.19%) aligned 0 times 1004s 9 (3.96%) aligned exactly 1 time 1004s 11 (4.85%) aligned >1 times 1004s 8.81% overall alignment rate 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s GA 1004s GA 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s CC 1004s CC 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s TCACGTG 1004s TCACGTG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s CCGAAAGACGGA 1004s CCGAAAGACGGA 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s CTCCTGTTCAC 1004s CTCCTGTTCAC 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s GACGGACG 1004s GACGGACG 1004s Processing line... 1004s Processing line... 1004s AC 1004s AC 1004s Processing line... 1004s GG 1004s GG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s CC 1004s CC 1004s Processing line... 1004s GC 1004s GC 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s GTAG 1004s GTAG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s ACCGAAAGACGGACG 1004s ACCGAAAGACGGACG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s CCCG 1004s CCCG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s GTATCG 1004s GTATCG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s CCG 1004s CCG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s CTGTTC 1004s CTGTTC 1004s Processing line... 1004s GACGGACG 1004s GACGGACG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s CTGTTCACGT 1004s CTGTTCACGT 1004s Processing line... 1004s GCGT 1004s GCGT 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s ATGACAACCGAAAGACGGACGTA 1004s ATGACAACCGAAAGACGGACGTA 1004s --- Summary --- 1004s Read 1 reference strings 1004s Checked 20 alignments, 0 edits 1004s --------------- 1004s PASSED 1004s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1004s /usr/bin/bowtie2 --trim3 6 --rdg 49.0701905824087 --trim5 7 --score-min L,4.79857853328771,7.02310421129868 --gbar 6 --large-index --np 6 --cp-min 2 --cp-ival 1 --mm -N 1 -L16 -q -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1004s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '1' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1004s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '7' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1004s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '8' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1004s Warning: skipping read '9' because length (1) <= # seed mismatches (1) 1004s Warning: skipping read '9' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1004s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '10' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1004s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '14' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1004s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '33' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1004s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '37' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1004s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '39' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1004s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '40' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1004s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '42' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1004s Warning: skipping read '44' because length (1) <= # seed mismatches (1) 1004s Warning: skipping read '44' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1004s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '45' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1004s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '46' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1004s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '49' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1004s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '52' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1004s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '53' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1004s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '55' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1004s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '65' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1004s Warning: skipping read '66' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '66' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1004s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '67' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1004s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '70' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1004s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '73' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1004s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '19' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1004s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '20' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1004s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '21' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1004s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '25' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1004s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '58' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1004s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '61' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1004s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '62' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1004s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '83' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1004s Warning: skipping read '87' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '87' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1004s Warning: skipping read '89' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '89' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1004s Warning: skipping read '90' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '90' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1004s Warning: skipping read '94' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '94' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1004s Warning: skipping read '95' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '95' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1004s Warning: skipping read '97' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '97' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1004s Warning: skipping read '98' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '98' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1004s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '99' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1004s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '100' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1004s Warning: skipping read '102' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '102' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1004s Warning: skipping read '103' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '103' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1004s Warning: skipping read '104' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '104' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1004s Warning: skipping read '105' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '105' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1004s Warning: skipping read '107' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '107' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1004s Warning: skipping read '109' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '109' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1004s Warning: skipping read '110' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '110' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1004s Warning: skipping read '113' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '113' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1004s Warning: skipping read '114' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '114' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1004s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '119' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1004s Warning: skipping read '123' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '123' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1004s Warning: skipping read '124' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '124' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1004s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '125' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1004s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '126' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1004s Warning: skipping read '129' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '129' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1004s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '75' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 1004s Warning: skipping read '145' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '145' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1004s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '29' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1004s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '31' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 1004s Warning: skipping read '161' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '161' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 1004s Warning: skipping read '163' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '163' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 1004s Warning: skipping read '165' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '165' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 1004s Warning: skipping read '167' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '167' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 1004s Warning: skipping read '172' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '172' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 1004s Warning: skipping read '177' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '177' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 1004s Warning: skipping read '178' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '178' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 1004s Warning: skipping read '179' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '179' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 1004s Warning: skipping read '149' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '149' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 1004s Warning: skipping read '150' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '150' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 1004s Warning: skipping read '151' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '151' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 1004s Warning: skipping read '153' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '153' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 1004s Warning: skipping read '154' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '154' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 1004s Warning: skipping read '158' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '158' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 1004s Warning: skipping read '160' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '160' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '193; setting to 0 instead 1004s Warning: skipping read '193' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '193' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '194; setting to 0 instead 1004s Warning: skipping read '194' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '194' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '195; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '196; setting to 0 instead 1004s Warning: skipping read '196' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '196' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '197; setting to 0 instead 1004s Warning: skipping read '197' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '197' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '198; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 1004s Warning: skipping read '139' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '139' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 1004s Warning: skipping read '140' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '140' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 1004s Warning: skipping read '141' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '141' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 1004s Warning: skipping read '142' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '142' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 1004s Warning: skipping read '143' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '143' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 1004s Warning: skipping read '183' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '183' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '189; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '190; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '191; setting to 0 instead 1004s Warning: skipping read '191' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '191' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '192; setting to 0 instead 1004s Warning: skipping read '192' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '192' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '225; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '226; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '227; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '199; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '200; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '201; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '202; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '203; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '204; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '205; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '206; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '209; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '210; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '211; setting to 0 instead 1004s Warning: skipping read '211' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '211' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '212; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '213; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '214; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '215; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '216; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '217; setting to 0 instead 1004s Warning: skipping read '217' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '217' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '218; setting to 0 instead 1004s Warning: skipping read '218' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '218' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '219; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '220; setting to 0 instead 1004s Warning: skipping read '220' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '220' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '221; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '222; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '223; setting to 0 instead 1004s Warning: skipping read '223' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '223' because it was < 2 characters long 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '224; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '207; setting to 0 instead 1004s Warning: minimum score function gave positive number in --end-to-end mode for read '208; setting to 0 instead 1004s Warning: skipping read '208' because length (0) <= # seed mismatches (1) 1004s Warning: skipping read '208' because it was < 2 characters long 1004s 227 reads; of these: 1004s 227 (100.00%) were unpaired; of these: 1004s 207 (91.19%) aligned 0 times 1004s 9 (3.96%) aligned exactly 1 time 1004s 11 (4.85%) aligned >1 times 1004s 8.81% overall alignment rate 1004s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1004s Flattened IUPAC characters 1004s Mutating sequence Sim.pm.2 1004s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1004s Finished SNPs 1004s Finished ref gaps 1004s Finished read gaps 1004s Mutating sequence Sim.pm.1 1004s Introducing 3 SNPs, 1/1 ref/read gaps, and 1 rearrangements 1004s Finished SNPs 1004s Finished ref gaps 1004s Finished read gaps 1004s Mutated reference genome to subject genome 1004s SNPs introduced: 5 1004s Reference gaps introduced: 1 1004s Read gaps introduced: 1 1004s Rearrangements introduced: 1 1004s Created read sampler 1004s Sampling 64 reads 1004s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1004s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1004s parsing sequence Sim.pm.1... 1004s parsing sequence Sim.pm.2... 1004s Parsed 81 reference bases 1004s *** Run 12 of 100 1004s /usr/bin/bowtie2 -D 4 -R 1 --np 4 --nofw --gbar 3 --score-min L,4.46258613435543,1.08783036678358 --cp-ival 1 --cp-min 2 --large-index -M 5 --rdg 20.0755085374314 --trim3 1 --mp 7.94716308941546,6.48676788172464 --local -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1004s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1004s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 1004s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1004s 64 reads; of these: 1004s 63 (98.44%) were paired; of these: 1004s 62 (98.41%) aligned concordantly 0 times 1004s 1 (1.59%) aligned concordantly exactly 1 time 1004s 0 (0.00%) aligned concordantly >1 times 1004s ---- 1004s 62 pairs aligned concordantly 0 times; of these: 1004s 2 (3.23%) aligned discordantly 1 time 1004s ---- 1004s 60 pairs aligned 0 times concordantly or discordantly; of these: 1004s 120 mates make up the pairs; of these: 1004s 107 (89.17%) aligned 0 times 1004s 11 (9.17%) aligned exactly 1 time 1004s 2 (1.67%) aligned >1 times 1004s 1 (1.56%) were unpaired; of these: 1004s 1 (100.00%) aligned 0 times 1004s 0 (0.00%) aligned exactly 1 time 1004s 0 (0.00%) aligned >1 times 1004s 14.96% overall alignment rate 1004s Read 50 alignments... 1004s Read 100 alignments... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s ATCCCGTATCGCGTAGGGATGACAACCGAAAGACGGACGTAAATCC 1004s ATCCCGTATCGCGTAGNGATGACAACCGAAAGACGGACGTANAT-C 1004s Processing line... 1004s AACCGAAAGACG 1004s AACCGAAAGACG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s TATCGCGTAGGGATGACAACCGAAAG 1004s TATCGCGTAGNGATGACAACCGAAAG 1004s Processing line... 1004s ATCGCG 1004s ATCGCG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s GTATCGCGTAGGGATGACAACCGAAAGACGGACGTAAATCC 1004s GTATCGCGTAGNGATGACAACCGAAAGACGGACGTANAT-C 1004s Processing line... 1004s AACCGAAAGACGGACG 1004s AACCGAAAGACGGACG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s AACCGAAA 1004s AACCGAAA 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s CCGAAAGAC 1004s CCGAAAGAC 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s AAAGACGGACGT 1004s AAAGACGGACGT 1004s Processing line... 1004s Processing line... 1004s GGACGTA 1004s GGACGTA 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s ATCCCGTATCGCGTAGGGATGACAACCGAAAGACGGACGTAAATCC 1004s ATCCCGTATCGCGTAGNGATGACAACCGAAAGACGGACGTANAT-C 1004s Processing line... 1004s CCCGTATCGCGTAG 1004s CCCGTATCGCGTAG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s GGAC 1004s GGAC 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s ACAACCGAAA 1004s ACAACCGAAA 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s GATGACAACCGAAAGACGGACGTAAATCCCG 1004s GATGACAACCGAAAGACGGACGTANATCCCG 1004s Processing line... 1004s GTAGGGATGACAA 1004s GTAGNGATGACAA 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s CCGAAAGACG 1004s CCGAAAGACG 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s ATCCCGTATCGCGTAGGGATGACAACCGAAAGACGGACGT 1004s ATCCCGTATCGCGTAGNGATGACAACCGAAAGACGGACGT 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s GTAGGGATGACAACCGAAAGACGGACGTAA 1004s GTAGNGATGACAACCGAAAGACGGACGT-A 1004s Processing line... 1004s --- Summary --- 1004s Read 1 reference strings 1004s Checked 19 alignments, 0 edits 1004s --------------- 1004s PASSED 1004s Flattened IUPAC characters 1004s Mutating sequence Sim.pm.1 1004s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1004s Finished SNPs 1004s Finished ref gaps 1004s Finished read gaps 1004s Mutating sequence Sim.pm.2 1004s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1004s Finished SNPs 1004s Finished ref gaps 1004s Finished read gaps 1004s Mutated reference genome to subject genome 1004s SNPs introduced: 7 1004s Reference gaps introduced: 0 1004s Read gaps introduced: 1 1004s Rearrangements introduced: 0 1004s Created read sampler 1004s Sampling 128 reads 1004s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1004s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1004s *** Run 13 of 100 1004s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mm --trim3 2 --mp 8.49015106291642,1.44476376557952 --rdg 1.0388126551635 --local --n-ceil 1.03302827421921,1.24959574230744 --large-index -M 3 --score-min L,9.04641589193854,6.810963535184 --gbar 5 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1004s parsing sequence Sim.pm.1... 1004s parsing sequence Sim.pm.2... 1004s Parsed 81 reference bases 1004s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1004s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1004s Warning: skipping read '3' because it was < 2 characters long 1004s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1004s Warning: skipping read '8' because it was < 2 characters long 1004s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 1004s Warning: skipping read '38' because it was < 2 characters long 1004s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1004s Warning: skipping read '39' because it was < 2 characters long 1004s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1004s Warning: skipping read '46' because it was < 2 characters long 1004s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1004s Warning: skipping read '51' because it was < 2 characters long 1004s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1004s Warning: skipping read '80' because it was < 2 characters long 1004s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1004s Warning: skipping read '97' because it was < 2 characters long 1004s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 1004s Warning: skipping read '102' because it was < 2 characters long 1004s 128 reads; of these: 1004s 128 (100.00%) were unpaired; of these: 1004s 128 (100.00%) aligned 0 times 1004s 0 (0.00%) aligned exactly 1 time 1004s 0 (0.00%) aligned >1 times 1004s 0.00% overall alignment rate 1004s Read 50 alignments... 1004s Read 100 alignments... 1004s Processing line... 1004s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mm --trim3 2 --mp 8.49015106291642,1.44476376557952 --rdg 1.0388126551635 --local --n-ceil 1.03302827421921,1.24959574230744 --large-index -M 3 --score-min L,9.04641589193854,6.810963535184 --gbar 5 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s Processing line... 1004s --- Summary --- 1004s Read 1 reference strings 1004s Checked 0 alignments, 0 edits 1004s --------------- 1004s PASSED 1004s ALSO checking that bowtie2 and bowtie2-align match up 1005s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1005s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '3' because it was < 2 characters long 1005s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '8' because it was < 2 characters long 1005s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 1005s Warning: skipping read '38' because it was < 2 characters long 1005s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '39' because it was < 2 characters long 1005s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '46' because it was < 2 characters long 1005s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '51' because it was < 2 characters long 1005s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '80' because it was < 2 characters long 1005s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '97' because it was < 2 characters long 1005s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 1005s Warning: skipping read '102' because it was < 2 characters long 1005s 128 reads; of these: 1005s 128 (100.00%) were unpaired; of these: 1005s 128 (100.00%) aligned 0 times 1005s 0 (0.00%) aligned exactly 1 time 1005s 0 (0.00%) aligned >1 times 1005s 0.00% overall alignment rate 1005s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1005s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1005s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mm --trim3 2 --mp 8.49015106291642,1.44476376557952 --rdg 1.0388126551635 --local --n-ceil 1.03302827421921,1.24959574230744 --large-index -M 3 --score-min L,9.04641589193854,6.810963535184 --gbar 5 -r -p 3 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1005s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1005s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '3' because it was < 2 characters long 1005s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '8' because it was < 2 characters long 1005s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 1005s Warning: skipping read '38' because it was < 2 characters long 1005s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '39' because it was < 2 characters long 1005s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '46' because it was < 2 characters long 1005s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '51' because it was < 2 characters long 1005s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '80' because it was < 2 characters long 1005s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '97' because it was < 2 characters long 1005s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 1005s Warning: skipping read '102' because it was < 2 characters long 1005s 128 reads; of these: 1005s 128 (100.00%) were unpaired; of these: 1005s 128 (100.00%) aligned 0 times 1005s 0 (0.00%) aligned exactly 1 time 1005s 0 (0.00%) aligned >1 times 1005s 0.00% overall alignment rate 1005s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1005s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1005s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1005s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1005s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mm --trim3 2 --mp 8.49015106291642,1.44476376557952 --rdg 1.0388126551635 --local --n-ceil 1.03302827421921,1.24959574230744 --large-index -M 3 --score-min L,9.04641589193854,6.810963535184 --gbar 5 -r -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1005s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1005s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '3' because it was < 2 characters long 1005s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '8' because it was < 2 characters long 1005s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '51' because it was < 2 characters long 1005s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '80' because it was < 2 characters long 1005s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 1005s Warning: skipping read '38' because it was < 2 characters long 1005s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '39' because it was < 2 characters long 1005s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1005s Warning: skipping read '46' because it was < 2 characters long 1005s Warning: skipping read '97' because it was < 2 characters long 1005s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 1005s Warning: skipping read '102' because it was < 2 characters long 1005s 128 reads; of these: 1005s 128 (100.00%) were unpaired; of these: 1005s 128 (100.00%) aligned 0 times 1005s 0 (0.00%) aligned exactly 1 time 1005s 0 (0.00%) aligned >1 times 1005s 0.00% overall alignment rate 1005s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1005s Flattened IUPAC characters 1005s Mutating sequence Sim.pm.2 1005s Introducing 2 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1005s Finished SNPs 1005s Finished ref gaps 1005s Finished read gaps 1005s Mutating sequence Sim.pm.1 1005s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1005s Finished SNPs 1005s Finished ref gaps 1005s Finished read gaps 1005s Mutated reference genome to subject genome 1005s SNPs introduced: 5 1005s Reference gaps introduced: 0 1005s Read gaps introduced: 2 1005s Rearrangements introduced: 0 1005s Created read sampler 1005s Sampling 82 reads 1005s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1005s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1005s parsing sequence Sim.pm.1... 1005s parsing sequence Sim.pm.2... 1005s Parsed 81 reference bases 1005s *** Run 14 of 100 1005s /usr/bin/bowtie2 -k 2 --score-min L,3.07646307419025,7.35914549768314 --large-index --local --rfg 2.32558833326912,4.32070591825061 --rdg 20.0014243512978 -D 42 --cp-ival 2 --cp-min 2 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1005s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 1005s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1005s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 1005s Warning: skipping mate #2 of read '13' because it was < 2 characters long 1005s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 1005s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1005s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 1005s Warning: skipping mate #2 of read '37' because it was < 2 characters long 1005s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 1005s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1005s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 1005s Warning: skipping mate #2 of read '41' because it was < 2 characters long 1005s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 1005s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1005s Read 50 alignments... 1005s Read 100 alignments... 1005s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 1005s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1005s 82 reads; of these: 1005s 82 (100.00%) were paired; of these: 1005s 82 (100.00%) aligned concordantly 0 times 1005s 0 (0.00%) aligned concordantly exactly 1 time 1005s 0 (0.00%) aligned concordantly >1 times 1005s ---- 1005s 82 pairs aligned concordantly 0 times; of these: 1005s 0 (0.00%) aligned discordantly 1 time 1005s ---- 1005s 82 pairs aligned 0 times concordantly or discordantly; of these: 1005s 164 mates make up the pairs; of these: 1005s 164 (100.00%) aligned 0 times 1005s 0 (0.00%) aligned exactly 1 time 1005s 0 (0.00%) aligned >1 times 1005s 0.00% overall alignment rate 1005s Read 150 alignments... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s /usr/bin/bowtie2 -k 2 --score-min L,3.07646307419025,7.35914549768314 --large-index --local --rfg 2.32558833326912,4.32070591825061 --rdg 20.0014243512978 -D 42 --cp-ival 2 --cp-min 2 -r -p 3 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s Processing line... 1005s --- Summary --- 1005s Read 1 reference strings 1005s Checked 0 alignments, 0 edits 1005s --------------- 1005s PASSED 1005s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1006s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #2 of read '13' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #2 of read '37' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #2 of read '41' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1006s 82 reads; of these: 1006s 82 (100.00%) were paired; of these: 1006s 82 (100.00%) aligned concordantly 0 times 1006s 0 (0.00%) aligned concordantly exactly 1 time 1006s 0 (0.00%) aligned concordantly >1 times 1006s ---- 1006s 82 pairs aligned concordantly 0 times; of these: 1006s 0 (0.00%) aligned discordantly 1 time 1006s ---- 1006s 82 pairs aligned 0 times concordantly or discordantly; of these: 1006s 164 mates make up the pairs; of these: 1006s 164 (100.00%) aligned 0 times 1006s 0 (0.00%) aligned exactly 1 time 1006s 0 (0.00%) aligned >1 times 1006s 0.00% overall alignment rate 1006s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1006s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1006s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1006s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1006s /usr/bin/bowtie2 -k 2 --score-min L,3.07646307419025,7.35914549768314 --large-index --local --rfg 2.32558833326912,4.32070591825061 --rdg 20.0014243512978 -D 42 --cp-ival 2 --cp-min 2 -r -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1006s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #2 of read '13' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #2 of read '37' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #2 of read '41' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 1006s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1006s 82 reads; of these: 1006s 82 (100.00%) were paired; of these: 1006s 82 (100.00%) aligned concordantly 0 times 1006s 0 (0.00%) aligned concordantly exactly 1 time 1006s 0 (0.00%) aligned concordantly >1 times 1006s ---- 1006s 82 pairs aligned concordantly 0 times; of these: 1006s 0 (0.00%) aligned discordantly 1 time 1006s ---- 1006s 82 pairs aligned 0 times concordantly or discordantly; of these: 1006s 164 mates make up the pairs; of these: 1006s 164 (100.00%) aligned 0 times 1006s 0 (0.00%) aligned exactly 1 time 1006s 0 (0.00%) aligned >1 times 1006s 0.00% overall alignment rate 1006s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1006s Flattened IUPAC characters 1006s Mutating sequence Sim.pm.1 1006s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1006s Finished SNPs 1006s Finished ref gaps 1006s Finished read gaps 1006s Mutating sequence Sim.pm.2 1006s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1006s Finished SNPs 1006s Finished ref gaps 1006s Finished read gaps 1006s Mutated reference genome to subject genome 1006s SNPs introduced: 16 1006s Reference gaps introduced: 0 1006s Read gaps introduced: 1 1006s Rearrangements introduced: 0 1006s Created read sampler 1006s Sampling 78 reads 1006s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1006s *** Run 15 of 100 1006s /usr/bin/bowtie2 -N 1 -R 4 --norc --np 5 --n-ceil 0.644075125337758,1.46213732207272 --score-min L,7.69410296622606,4.34409065323309 --trim5 4 -i S,2.92956173513678 --mm --cp-ival 3 --cp-min 3 --large-index --rdg 19.6284382196224,14.4962046403333 --trim3 0 --local -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1006s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1006s parsing sequence Sim.pm.1... 1006s parsing sequence Sim.pm.2... 1006s Parsed 81 reference bases 1006s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '31' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (1) 1006s Warning: skipping mate #2 of read '34' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (1) 1006s Warning: skipping mate #2 of read '40' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (1) 1006s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '50' because it was < 2 characters long 1006s Read 50 alignments... 1006s Read 100 alignments... 1006s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1006s 78 reads; of these: 1006s 73 (93.59%) were paired; of these: 1006s 73 (100.00%) aligned concordantly 0 times 1006s 0 (0.00%) aligned concordantly exactly 1 time 1006s 0 (0.00%) aligned concordantly >1 times 1006s ---- 1006s 73 pairs aligned concordantly 0 times; of these: 1006s 0 (0.00%) aligned discordantly 1 time 1006s ---- 1006s 73 pairs aligned 0 times concordantly or discordantly; of these: 1006s 146 mates make up the pairs; of these: 1006s 146 (100.00%) aligned 0 times 1006s 0 (0.00%) aligned exactly 1 time 1006s 0 (0.00%) aligned >1 times 1006s 5 (6.41%) were unpaired; of these: 1006s 5 (100.00%) aligned 0 times 1006s 0 (0.00%) aligned exactly 1 time 1006s 0 (0.00%) aligned >1 times 1006s 0.00% overall alignment rate 1006s Read 150 alignments... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s /usr/bin/bowtie2 -N 1 -R 4 --norc --np 5 --n-ceil 0.644075125337758,1.46213732207272 --score-min L,7.69410296622606,4.34409065323309 --trim5 4 -i S,2.92956173513678 --mm --cp-ival 3 --cp-min 3 --large-index --rdg 19.6284382196224,14.4962046403333 --trim3 0 --local -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s Processing line... 1006s --- Summary --- 1006s Read 1 reference strings 1006s Checked 0 alignments, 0 edits 1006s --------------- 1006s PASSED 1006s ALSO checking that bowtie2 and bowtie2-align match up 1006s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '31' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (1) 1006s Warning: skipping mate #2 of read '34' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (1) 1006s Warning: skipping mate #2 of read '40' because it was < 2 characters long 1006s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (1) 1006s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1006s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (1) 1006s Warning: skipping mate #1 of read '50' because it was < 2 characters long 1007s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1007s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1007s 78 reads; of these: 1007s 73 (93.59%) were paired; of these: 1007s 73 (100.00%) aligned concordantly 0 times 1007s 0 (0.00%) aligned concordantly exactly 1 time 1007s 0 (0.00%) aligned concordantly >1 times 1007s ---- 1007s 73 pairs aligned concordantly 0 times; of these: 1007s 0 (0.00%) aligned discordantly 1 time 1007s ---- 1007s 73 pairs aligned 0 times concordantly or discordantly; of these: 1007s 146 mates make up the pairs; of these: 1007s 146 (100.00%) aligned 0 times 1007s 0 (0.00%) aligned exactly 1 time 1007s 0 (0.00%) aligned >1 times 1007s 5 (6.41%) were unpaired; of these: 1007s 5 (100.00%) aligned 0 times 1007s 0 (0.00%) aligned exactly 1 time 1007s 0 (0.00%) aligned >1 times 1007s 0.00% overall alignment rate 1007s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1007s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1007s /usr/bin/bowtie2 -N 1 -R 4 --norc --np 5 --n-ceil 0.644075125337758,1.46213732207272 --score-min L,7.69410296622606,4.34409065323309 --trim5 4 -i S,2.92956173513678 --mm --cp-ival 3 --cp-min 3 --large-index --rdg 19.6284382196224,14.4962046403333 --trim3 0 --local -q -p 4 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1007s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1007s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1007s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1007s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (1) 1007s Warning: skipping mate #2 of read '34' because it was < 2 characters long 1007s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1007s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1007s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (1) 1007s Warning: skipping mate #2 of read '40' because it was < 2 characters long 1007s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (1) 1007s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1007s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '31' because it was < 2 characters long 1007s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '50' because it was < 2 characters long 1007s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1007s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (1) 1007s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1007s 78 reads; of these: 1007s 73 (93.59%) were paired; of these: 1007s 73 (100.00%) aligned concordantly 0 times 1007s 0 (0.00%) aligned concordantly exactly 1 time 1007s 0 (0.00%) aligned concordantly >1 times 1007s ---- 1007s 73 pairs aligned concordantly 0 times; of these: 1007s 0 (0.00%) aligned discordantly 1 time 1007s ---- 1007s 73 pairs aligned 0 times concordantly or discordantly; of these: 1007s 146 mates make up the pairs; of these: 1007s 146 (100.00%) aligned 0 times 1007s 0 (0.00%) aligned exactly 1 time 1007s 0 (0.00%) aligned >1 times 1007s 5 (6.41%) were unpaired; of these: 1007s 5 (100.00%) aligned 0 times 1007s 0 (0.00%) aligned exactly 1 time 1007s 0 (0.00%) aligned >1 times 1007s 0.00% overall alignment rate 1007s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1007s Flattened IUPAC characters 1007s Mutating sequence Sim.pm.2 1007s Introducing 8 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1007s Finished SNPs 1007s Finished ref gaps 1007s Finished read gaps 1007s Mutating sequence Sim.pm.1 1007s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1007s Finished SNPs 1007s Finished ref gaps 1007s Finished read gaps 1007s Mutated reference genome to subject genome 1007s SNPs introduced: 12 1007s Reference gaps introduced: 1 1007s Read gaps introduced: 2 1007s Rearrangements introduced: 0 1007s Created read sampler 1007s Sampling 34 reads 1007s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1007s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1007s parsing sequence Sim.pm.1... 1007s parsing sequence Sim.pm.2... 1007s Parsed 81 reference bases 1007s *** Run 16 of 100 1007s /usr/bin/bowtie2 -N 0 -L19 --rfg 13.8319050263203,17.8746235158029 --gbar 1 --score-min L,9.58472583289337,1.40298199665429 --cp-min 9 --mm --cp-ival 1 --rdg 33.5387246756775,19.8716786979198 --mp 7.34060163421144,2.73469947066598 --local --large-index -M 6 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1007s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1007s 34 reads; of these: 1007s 34 (100.00%) were paired; of these: 1007s 34 (100.00%) aligned concordantly 0 times 1007s 0 (0.00%) aligned concordantly exactly 1 time 1007s 0 (0.00%) aligned concordantly >1 times 1007s ---- 1007s 34 pairs aligned concordantly 0 times; of these: 1007s 0 (0.00%) aligned discordantly 1 time 1007s ---- 1007s 34 pairs aligned 0 times concordantly or discordantly; of these: 1007s 68 mates make up the pairs; of these: 1007s 67 (98.53%) aligned 0 times 1007s 1 (1.47%) aligned exactly 1 time 1007s 0 (0.00%) aligned >1 times 1007s 1.47% overall alignment rate 1007s Read 50 alignments... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s TATCGCGTAGCGATGACAACCGAAAGACGGACGTA 1007s TATCGCGTAGNGATGACAACCGAAAGACGGACGTA 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s --- Summary --- 1007s Read 1 reference strings 1007s Checked 1 alignments, 0 edits 1007s --------------- 1007s PASSED 1007s Flattened IUPAC characters 1007s Mutating sequence Sim.pm.1 1007s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1007s *** Run 17 of 100 1007s /usr/bin/bowtie2 --large-index --local --trim3 8 --mp 6.7142454589302,3.66116675045303 -a --cp-ival 3 --mm --cp-min 2 --score-min L,2.21508201271387,4.12216350966315 --gbar 4 --rfg 40.4424587067259,7.77733826640703 --trim5 0 --np 5 -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta 1007s Finished SNPs 1007s Finished ref gaps 1007s Finished read gaps 1007s Mutating sequence Sim.pm.2 1007s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1007s Finished SNPs 1007s Finished ref gaps 1007s Finished read gaps 1007s Mutated reference genome to subject genome 1007s SNPs introduced: 5 1007s Reference gaps introduced: 1 1007s Read gaps introduced: 2 1007s Rearrangements introduced: 0 1007s Created read sampler 1007s Sampling 88 reads 1007s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1007s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1007s parsing sequence Sim.pm.1... 1007s parsing sequence Sim.pm.2... 1007s Parsed 81 reference bases 1007s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '1' because it was < 2 characters long 1007s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '2' because it was < 2 characters long 1007s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '8' because it was < 2 characters long 1007s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '13' because it was < 2 characters long 1007s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '16' because it was < 2 characters long 1007s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '26' because it was < 2 characters long 1007s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '28' because it was < 2 characters long 1007s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '29' because it was < 2 characters long 1007s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '33' because it was < 2 characters long 1007s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '40' because it was < 2 characters long 1007s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '54' because it was < 2 characters long 1007s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '60' because it was < 2 characters long 1007s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '71' because it was < 2 characters long 1007s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '72' because it was < 2 characters long 1007s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '74' because it was < 2 characters long 1007s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '75' because it was < 2 characters long 1007s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '79' because it was < 2 characters long 1007s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '86' because it was < 2 characters long 1007s 88 reads; of these: 1007s 88 (100.00%) were unpaired; of these: 1007s 88 (100.00%) aligned 0 times 1007s 0 (0.00%) aligned exactly 1 time 1007s 0 (0.00%) aligned >1 times 1007s 0.00% overall alignment rate 1007s Read 50 alignments... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s Processing line... 1007s --- Summary --- 1007s Read 1 reference strings 1007s Checked 0 alignments, 0 edits 1007s --------------- 1007s PASSED 1007s ALSO checking that bowtie2 and bowtie2-align match up 1007s /usr/bin/bowtie2 --large-index --local --trim3 8 --mp 6.7142454589302,3.66116675045303 -a --cp-ival 3 --mm --cp-min 2 --score-min L,2.21508201271387,4.12216350966315 --gbar 4 --rfg 40.4424587067259,7.77733826640703 --trim5 0 --np 5 -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1007s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '1' because it was < 2 characters long 1007s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '2' because it was < 2 characters long 1007s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '8' because it was < 2 characters long 1007s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '13' because it was < 2 characters long 1007s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '16' because it was < 2 characters long 1007s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '26' because it was < 2 characters long 1007s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '28' because it was < 2 characters long 1007s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '29' because it was < 2 characters long 1007s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '33' because it was < 2 characters long 1007s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '40' because it was < 2 characters long 1007s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '54' because it was < 2 characters long 1007s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '60' because it was < 2 characters long 1007s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '71' because it was < 2 characters long 1007s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '72' because it was < 2 characters long 1007s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '74' because it was < 2 characters long 1007s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '75' because it was < 2 characters long 1007s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '79' because it was < 2 characters long 1007s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1007s Warning: skipping read '86' because it was < 2 characters long 1007s 88 reads; of these: 1007s 88 (100.00%) were unpaired; of these: 1007s 88 (100.00%) aligned 0 times 1007s 0 (0.00%) aligned exactly 1 time 1007s 0 (0.00%) aligned >1 times 1007s 0.00% overall alignment rate 1007s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1007s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1007s /usr/bin/bowtie2 --large-index --local --trim3 8 --mp 6.7142454589302,3.66116675045303 -a --cp-ival 3 --mm --cp-min 2 --score-min L,2.21508201271387,4.12216350966315 --gbar 4 --rfg 40.4424587067259,7.77733826640703 --trim5 0 --np 5 -f -p 3 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1008s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '1' because it was < 2 characters long 1008s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '2' because it was < 2 characters long 1008s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '8' because it was < 2 characters long 1008s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '13' because it was < 2 characters long 1008s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '16' because it was < 2 characters long 1008s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '26' because it was < 2 characters long 1008s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '28' because it was < 2 characters long 1008s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '29' because it was < 2 characters long 1008s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '33' because it was < 2 characters long 1008s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '40' because it was < 2 characters long 1008s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '71' because it was < 2 characters long 1008s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '72' because it was < 2 characters long 1008s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '74' because it was < 2 characters long 1008s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '75' because it was < 2 characters long 1008s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '79' because it was < 2 characters long 1008s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '86' because it was < 2 characters long 1008s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '54' because it was < 2 characters long 1008s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read '60' because it was < 2 characters long 1008s 88 reads; of these: 1008s 88 (100.00%) were unpaired; of these: 1008s 88 (100.00%) aligned 0 times 1008s 0 (0.00%) aligned exactly 1 time 1008s 0 (0.00%) aligned >1 times 1008s 0.00% overall alignment rate 1008s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1008s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1008s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1008s Flattened IUPAC characters 1008s Mutating sequence Sim.pm.2 1008s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1008s Finished SNPs 1008s Finished ref gaps 1008s Finished read gaps 1008s Mutating sequence Sim.pm.1 1008s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1008s Finished SNPs 1008s Finished ref gaps 1008s Finished read gaps 1008s Mutated reference genome to subject genome 1008s SNPs introduced: 9 1008s Reference gaps introduced: 1 1008s Read gaps introduced: 0 1008s Rearrangements introduced: 1 1008s Created read sampler 1008s Sampling 51 reads 1008s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1008s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1008s parsing sequence Sim.pm.1... 1008s parsing sequence Sim.pm.2... 1008s Parsed 81 reference bases 1008s *** Run 18 of 100 1008s /usr/bin/bowtie2 --score-min L,9.50613623811937,2.57268038982425 --rfg 34.5969285381674 -N 1 -L31 -D 10 --np 1 --large-index -a --trim3 0 --rdg 48.0273695976131,7.73689364997482 --local --cp-ival 1 --mm --cp-min 3 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1008s Warning: skipping read '5' because length (1) <= # seed mismatches (1) 1008s Warning: skipping read '5' because it was < 2 characters long 1008s Warning: skipping read '22' because length (1) <= # seed mismatches (1) 1008s Warning: skipping read '22' because it was < 2 characters long 1008s Warning: skipping read '44' because length (1) <= # seed mismatches (1) 1008s Warning: skipping read '44' because it was < 2 characters long 1008s 51 reads; of these: 1008s 51 (100.00%) were unpaired; of these: 1008s 51 (100.00%) aligned 0 times 1008s 0 (0.00%) aligned exactly 1 time 1008s 0 (0.00%) aligned >1 times 1008s 0.00% overall alignment rate 1008s Read 50 alignments... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s Processing line... 1008s --- Summary --- 1008s Read 1 reference strings 1008s Checked 0 alignments, 0 edits 1008s --------------- 1008s PASSED 1008s ALSO checking that bowtie2 and bowtie2-align match up 1008s /usr/bin/bowtie2 --score-min L,9.50613623811937,2.57268038982425 --rfg 34.5969285381674 -N 1 -L31 -D 10 --np 1 --large-index -a --trim3 0 --rdg 48.0273695976131,7.73689364997482 --local --cp-ival 1 --mm --cp-min 3 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1008s Warning: skipping read '5' because length (1) <= # seed mismatches (1) 1008s Warning: skipping read '5' because it was < 2 characters long 1008s Warning: skipping read '22' because length (1) <= # seed mismatches (1) 1008s Warning: skipping read '22' because it was < 2 characters long 1008s Warning: skipping read '44' because length (1) <= # seed mismatches (1) 1008s Warning: skipping read '44' because it was < 2 characters long 1008s 51 reads; of these: 1008s 51 (100.00%) were unpaired; of these: 1008s 51 (100.00%) aligned 0 times 1008s 0 (0.00%) aligned exactly 1 time 1008s 0 (0.00%) aligned >1 times 1008s 0.00% overall alignment rate 1008s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1008s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1008s /usr/bin/bowtie2 --score-min L,9.50613623811937,2.57268038982425 --rfg 34.5969285381674 -N 1 -L31 -D 10 --np 1 --large-index -a --trim3 0 --rdg 48.0273695976131,7.73689364997482 --local --cp-ival 1 --mm --cp-min 3 -q -p 3 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1008s Warning: skipping read '5' because length (1) <= # seed mismatches (1) 1008s Warning: skipping read '5' because it was < 2 characters long 1008s Warning: skipping read '22' because length (1) <= # seed mismatches (1) 1008s Warning: skipping read '22' because it was < 2 characters long 1008s Warning: skipping read '44' because length (1) <= # seed mismatches (1) 1008s Warning: skipping read '44' because it was < 2 characters long 1008s 51 reads; of these: 1008s 51 (100.00%) were unpaired; of these: 1008s 51 (100.00%) aligned 0 times 1008s 0 (0.00%) aligned exactly 1 time 1008s 0 (0.00%) aligned >1 times 1008s 0.00% overall alignment rate 1008s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1008s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1008s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1008s Flattened IUPAC characters 1008s Mutating sequence Sim.pm.2 1008s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1008s Finished SNPs 1008s Finished ref gaps 1008s Finished read gaps 1008s Mutating sequence Sim.pm.1 1008s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1008s Finished SNPs 1008s Finished ref gaps 1008s Finished read gaps 1008s Mutated reference genome to subject genome 1008s SNPs introduced: 8 1008s Reference gaps introduced: 1 1008s Read gaps introduced: 1 1008s Rearrangements introduced: 0 1008s Created read sampler 1008s Sampling 127 reads 1008s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1008s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1008s parsing sequence Sim.pm.1... 1008s parsing sequence Sim.pm.2... 1008s Parsed 81 reference bases 1008s *** Run 19 of 100 1008s /usr/bin/bowtie2 --rdg 36.1109096801036 -a --trim3 4 --large-index --ma 12.3914249182079 --cp-min 4 --mm --cp-ival 1 --trim5 3 --score-min L,4.91018477704642,6.99953627258566 -R 1 --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq 1008s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1008s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s Warning: skipping mate #2 of read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 1008s Warning: skipping mate #2 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Read 50 alignments... 1008s 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 1008s 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 1008s 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 1008s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Read 100 alignments... 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 1008s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 1008s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1008s 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 1009s 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 1009s 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 1009s Read 150 alignments... 1009s Read 200 alignments... 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 127 reads; of these: 1009s 110 (86.61%) were paired; of these: 1009s 108 (98.18%) aligned concordantly 0 times 1009s 1 (0.91%) aligned concordantly exactly 1 time 1009s 1 (0.91%) aligned concordantly >1 times 1009s ---- 1009s 108 pairs aligned concordantly 0 times; of these: 1009s 0 (0.00%) aligned discordantly 1 time 1009s ---- 1009s 108 pairs aligned 0 times concordantly or discordantly; of these: 1009s 216 mates make up the pairs; of these: 1009s 197 (91.20%) aligned 0 times 1009s 7 (3.24%) aligned exactly 1 time 1009s 12 (5.56%) aligned >1 times 1009s 17 (13.39%) were unpaired; of these: 1009s 16 (94.12%) aligned 0 times 1009s 1 (5.88%) aligned exactly 1 time 1009s 0 (0.00%) aligned >1 times 1009s 10.13% overall alignment rate 1009s Read 250 alignments... 1009s Read 300 alignments... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GACAACCGAAAGACGG 1009s GACAACCGAAAGACGG 1009s Processing line... 1009s Processing line... 1009s CCCG 1009s CCCG 1009s Processing line... 1009s CCCG 1009s CCCG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GTA 1009s GTA 1009s Processing line... 1009s GTA 1009s GTA 1009s Processing line... 1009s GTA 1009s GTA 1009s Processing line... 1009s GTA 1009s GTA 1009s Processing line... 1009s GTA 1009s GTA 1009s Processing line... 1009s Processing line... 1009s GACAACCGA 1009s GACAACCGA 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s TCC 1009s TCC 1009s Processing line... 1009s TCC 1009s TCC 1009s Processing line... 1009s TCC 1009s TCC 1009s Processing line... 1009s GGA 1009s GGA 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GACAAC 1009s GACAAC 1009s Processing line... 1009s Processing line... 1009s CGCG 1009s CGCG 1009s Processing line... 1009s CGCG 1009s CGCG 1009s Processing line... 1009s CGCG 1009s CGCG 1009s Processing line... 1009s CGCG 1009s CGCG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CGTATCGC 1009s CGTATCGC 1009s Processing line... 1009s CGTATCGC 1009s CGTATCGC 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GA 1009s GA 1009s Processing line... 1009s GA 1009s GA 1009s Processing line... 1009s GA 1009s GA 1009s Processing line... 1009s GA 1009s GA 1009s Processing line... 1009s TC 1009s TC 1009s Processing line... 1009s TC 1009s TC 1009s Processing line... 1009s GA 1009s GA 1009s Processing line... 1009s GA 1009s GA 1009s Processing line... 1009s TC 1009s TC 1009s Processing line... 1009s TC 1009s TC 1009s Processing line... 1009s TC 1009s TC 1009s Processing line... 1009s TC 1009s TC 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GTATCGCG 1009s GTATCGCG 1009s Processing line... 1009s GTATCGCG 1009s GTATCGCG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GGACG 1009s GGACG 1009s Processing line... 1009s AAGACGGACG 1009s AAGACGGACG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CGTATCGCGT 1009s CGTATCGCGT 1009s Processing line... 1009s CGTATCGCGT 1009s CGTATCGCGT 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GTATCGCGT 1009s GTATCGCGT 1009s Processing line... 1009s GTATCGCGT 1009s GTATCGCGT 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s AAGACG 1009s AAGACG 1009s Processing line... 1009s Processing line... 1009s ATGACAACCGA 1009s ATGACAACCGA 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s AA 1009s AA 1009s Processing line... 1009s TT 1009s TT 1009s Processing line... 1009s AA 1009s AA 1009s Processing line... 1009s AA 1009s AA 1009s Processing line... 1009s CCGAAAGACGGACGT 1009s CCGAAAGACGGACGT 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CC 1009s CC 1009s Processing line... 1009s GG 1009s GG 1009s Processing line... 1009s CC 1009s CC 1009s Processing line... 1009s CC 1009s CC 1009s Processing line... 1009s CC 1009s CC 1009s Processing line... 1009s GG 1009s GG 1009s Processing line... 1009s GG 1009s GG 1009s Processing line... 1009s CC 1009s CC 1009s Processing line... 1009s CC 1009s CC 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CAACCGAAAGA 1009s CAACCGAAAGA 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CGGA 1009s CGGA 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CGCGT 1009s CGCGT 1009s Processing line... 1009s CGCGTAG 1009s CGCGTAG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s --- Summary --- 1009s Read 1 reference strings 1009s Checked 84 alignments, 0 edits 1009s --------------- 1009s PASSED 1009s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1009s /usr/bin/bowtie2 --rdg 36.1109096801036 -a --trim3 4 --large-index --ma 12.3914249182079 --cp-min 4 --mm --cp-ival 1 --trim5 3 --score-min L,4.91018477704642,6.99953627258566 -R 1 --qseq -p 4 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1009s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1009s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s Warning: skipping mate #2 of read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 1009s Warning: skipping mate #2 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 1009s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 1009s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 127 reads; of these: 1009s 110 (86.61%) were paired; of these: 1009s 108 (98.18%) aligned concordantly 0 times 1009s 1 (0.91%) aligned concordantly exactly 1 time 1009s 1 (0.91%) aligned concordantly >1 times 1009s ---- 1009s 108 pairs aligned concordantly 0 times; of these: 1009s 0 (0.00%) aligned discordantly 1 time 1009s ---- 1009s 108 pairs aligned 0 times concordantly or discordantly; of these: 1009s 216 mates make up the pairs; of these: 1009s 197 (91.20%) aligned 0 times 1009s 7 (3.24%) aligned exactly 1 time 1009s 12 (5.56%) aligned >1 times 1009s 17 (13.39%) were unpaired; of these: 1009s 16 (94.12%) aligned 0 times 1009s 1 (5.88%) aligned exactly 1 time 1009s 0 (0.00%) aligned >1 times 1009s 10.13% overall alignment rate 1009s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1009s Flattened IUPAC characters 1009s Mutating sequence Sim.pm.1 1009s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1009s Finished SNPs 1009s Finished ref gaps 1009s Finished read gaps 1009s Mutating sequence Sim.pm.2 1009s Introducing 9 SNPs, 0/2 ref/read gaps, and 1 rearrangements 1009s Finished SNPs 1009s Finished ref gaps 1009s Finished read gaps 1009s Mutated reference genome to subject genome 1009s SNPs introduced: 10 1009s Reference gaps introduced: 1 1009s Read gaps introduced: 2 1009s Rearrangements introduced: 1 1009s Created read sampler 1009s Sampling 127 reads 1009s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1009s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1009s parsing sequence Sim.pm.1... 1009s parsing sequence Sim.pm.2... 1009s Parsed 81 reference bases 1009s *** Run 20 of 100 1009s /usr/bin/bowtie2 --gbar 4 --score-min L,7.19688213883666,6.57815275394497 -k 13 --large-index -i C,3.10127127617973,12.8990775143828 --rfg 47.1135804162614,10.4604788702637 --trim3 0 --mp 8.00590732484224,4.74214310156282 --cp-ival 1 --np 4 --cp-min 7 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 1009s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 1009s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1009s 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 1009s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 1009s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 1009s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s Read 50 alignments... 1009s Read 100 alignments... 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 127 reads; of these: 1009s 127 (100.00%) were unpaired; of these: 1009s 98 (77.17%) aligned 0 times 1009s 15 (11.81%) aligned exactly 1 time 1009s 14 (11.02%) aligned >1 times 1009s 22.83% overall alignment rate 1009s Read 150 alignments... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s CG 1009s CG 1009s Processing line... 1009s Processing line... 1009s CGTATCGC 1009s CGTATCGC 1009s Processing line... 1009s CGTATCGC 1009s CGTATCGC 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GGCGAC 1009s GGCGAC 1009s Processing line... 1009s TA 1009s TA 1009s Processing line... 1009s TA 1009s TA 1009s Processing line... 1009s TA 1009s TA 1009s Processing line... 1009s TA 1009s TA 1009s Processing line... 1009s TA 1009s TA 1009s Processing line... 1009s TA 1009s TA 1009s Processing line... 1009s TA 1009s TA 1009s Processing line... 1009s TA 1009s TA 1009s Processing line... 1009s TA 1009s TA 1009s Processing line... 1009s TA 1009s TA 1009s Processing line... 1009s Processing line... 1009s GTTC 1009s GTTC 1009s Processing line... 1009s GC 1009s GC 1009s Processing line... 1009s GC 1009s GC 1009s Processing line... 1009s GC 1009s GC 1009s Processing line... 1009s GC 1009s GC 1009s Processing line... 1009s GC 1009s GC 1009s Processing line... 1009s GC 1009s GC 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s TCACGTGGGCGACG 1009s TCACGTGGGCGACG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s ATC 1009s ATC 1009s Processing line... 1009s ATC 1009s ATC 1009s Processing line... 1009s GAT 1009s GAT 1009s Processing line... 1009s ATC 1009s ATC 1009s Processing line... 1009s ATC 1009s ATC 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CTGTTCACGTGGGCG 1009s CTGTTCACGTGGGCG 1009s Processing line... 1009s CGAAAGA 1009s CGAAAGA 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GTATCGCGT 1009s GTATCGCGT 1009s Processing line... 1009s GTATCGCGT 1009s GTATCGCGT 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CCCGTATCG 1009s CCCGTATCG 1009s Processing line... 1009s CCCGTATCG 1009s CCCGTATCG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CTGTTCACGTGGGCG 1009s CTGTTCACGTGGGCG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GGCGAC 1009s GGCGAC 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GGG 1009s GGG 1009s Processing line... 1009s CCC 1009s CCC 1009s Processing line... 1009s CCC 1009s CCC 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CTCCT 1009s CTCCT 1009s Processing line... 1009s CCGTATCG 1009s CCGTATCG 1009s Processing line... 1009s CCGTATCG 1009s CCGTATCG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GTA 1009s GTA 1009s Processing line... 1009s GTA 1009s GTA 1009s Processing line... 1009s GTA 1009s GTA 1009s Processing line... 1009s GTA 1009s GTA 1009s Processing line... 1009s GTA 1009s GTA 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CGGACG 1009s CGGACG 1009s Processing line... 1009s CCGTAT 1009s CCGTAT 1009s Processing line... 1009s CCGTAT 1009s CCGTAT 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s TGG 1009s TGG 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s GAAAGAC 1009s GAAAGAC 1009s Processing line... 1009s TGTTCACGTG 1009s TGTTCACGTG 1009s Processing line... 1009s Processing line... 1009s TAT 1009s TAT 1009s Processing line... 1009s TAT 1009s TAT 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CCCG 1009s CCCG 1009s Processing line... 1009s CCCG 1009s CCCG 1009s Processing line... 1009s TGTTC 1009s TGTTC 1009s Processing line... 1009s Processing line... 1009s TGACAACC 1009s TGACAACC 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s CCGAAAGACGGAC 1009s CCGAAAGACGGAC 1009s Processing line... 1009s /usr/bin/bowtie2 --gbar 4 --score-min L,7.19688213883666,6.57815275394497 -k 13 --large-index -i C,3.10127127617973,12.8990775143828 --rfg 47.1135804162614,10.4604788702637 --trim3 0 --mp 8.00590732484224,4.74214310156282 --cp-ival 1 --np 4 --cp-min 7 --qseq -p 3 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s Processing line... 1009s --- Summary --- 1009s Read 1 reference strings 1009s Checked 84 alignments, 0 edits 1009s --------------- 1009s PASSED 1009s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1009s 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 1010s 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 1010s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1010s 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 1010s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 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 1010s 127 reads; of these: 1010s 127 (100.00%) were unpaired; of these: 1010s 98 (77.17%) aligned 0 times 1010s 15 (11.81%) aligned exactly 1 time 1010s 14 (11.02%) aligned >1 times 1010s 22.83% overall alignment rate 1010s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1010s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1010s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1010s Flattened IUPAC characters 1010s Mutating sequence Sim.pm.2 1010s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1010s Finished SNPs 1010s Finished ref gaps 1010s Finished read gaps 1010s Mutating sequence Sim.pm.1 1010s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1010s Finished SNPs 1010s Finished ref gaps 1010s Finished read gaps 1010s Mutated reference genome to subject genome 1010s SNPs introduced: 9 1010s Reference gaps introduced: 0 1010s Read gaps introduced: 0 1010s Rearrangements introduced: 0 1010s Created read sampler 1010s Sampling 111 reads 1010s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1010s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1010s parsing sequence Sim.pm.1... 1010s parsing sequence Sim.pm.2... 1010s Parsed 81 reference bases 1010s *** Run 21 of 100 1010s /usr/bin/bowtie2 --trim5 6 --score-min L,4.84013732681595,6.79334195770047 --n-ceil 0.889734035417155,0.869457309788033 --nofw -R 4 --mp 8.58806853927012,5.78825676487844 --large-index -M 3 --cp-min 3 --cp-ival 1 --mm -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1010s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1010s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '0' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1010s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '5' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1010s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '8' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1010s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '9' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1010s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '14' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1010s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '23' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1010s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read '25' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1010s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '28' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1010s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read '36' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1010s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '43' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1010s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '45' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1010s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '48' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1010s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read '55' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1010s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '60' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1010s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '67' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1010s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '69' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1010s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '70' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1010s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read '81' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1010s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '110' because it was < 2 characters long 1010s 111 reads; of these: 1010s 111 (100.00%) were unpaired; of these: 1010s 100 (90.09%) aligned 0 times 1010s 5 (4.50%) aligned exactly 1 time 1010s 6 (5.41%) aligned >1 times 1010s 9.91% overall alignment rate 1010s Read 50 alignments... 1010s Read 100 alignments... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s ACGTA 1010s ACGTA 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s CGCGTAG 1010s CGCGTAG 1010s Processing line... 1010s GACG 1010s GACG 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s /usr/bin/bowtie2 --trim5 6 --score-min L,4.84013732681595,6.79334195770047 --n-ceil 0.889734035417155,0.869457309788033 --nofw -R 4 --mp 8.58806853927012,5.78825676487844 --large-index -M 3 --cp-min 3 --cp-ival 1 --mm -r -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s CGTATC 1010s CGTATC 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s TTC 1010s TTC 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s GACAACCGAAAG 1010s GACAACCGAAAG 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s GGG 1010s GGG 1010s Processing line... 1010s Processing line... 1010s ACCG 1010s ACCG 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s CGT 1010s CGT 1010s Processing line... 1010s Processing line... 1010s GTAG 1010s GTAG 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s CGT 1010s CGT 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s --- Summary --- 1010s Read 1 reference strings 1010s Checked 11 alignments, 0 edits 1010s --------------- 1010s PASSED 1010s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1010s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1010s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '0' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1010s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '5' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1010s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '8' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1010s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '9' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1010s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '14' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1010s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '23' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1010s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read '25' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1010s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read '36' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1010s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '43' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1010s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '45' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1010s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '48' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1010s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '28' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1010s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '67' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1010s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '69' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1010s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '70' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1010s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read '81' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1010s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read '55' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1010s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '60' because it was < 2 characters long 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1010s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1010s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '110' because it was < 2 characters long 1010s 111 reads; of these: 1010s 111 (100.00%) were unpaired; of these: 1010s 100 (90.09%) aligned 0 times 1010s 5 (4.50%) aligned exactly 1 time 1010s 6 (5.41%) aligned >1 times 1010s 9.91% overall alignment rate 1010s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1010s Flattened IUPAC characters 1010s Mutating sequence Sim.pm.2 1010s Introducing 8 SNPs, 0/1 ref/read gaps, and 2 rearrangements 1010s Finished SNPs 1010s Finished ref gaps 1010s Finished read gaps 1010s Mutating sequence Sim.pm.1 1010s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1010s Finished SNPs 1010s Finished ref gaps 1010s Finished read gaps 1010s Mutated reference genome to subject genome 1010s SNPs introduced: 8 1010s Reference gaps introduced: 0 1010s Read gaps introduced: 1 1010s Rearrangements introduced: 2 1010s Created read sampler 1010s Sampling 144 reads 1010s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1010s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1010s parsing sequence Sim.pm.1... 1010s parsing sequence Sim.pm.2... 1010s Parsed 81 reference bases 1010s *** Run 22 of 100 1010s /usr/bin/bowtie2 --large-index -M 2 --trim3 8 --mp 8.3206353836013,6.04244940476874 --rdg 13.3625473984594,13.3481433655099 --local --cp-ival 2 --mm --cp-min 5 --score-min L,2.19352946497966,6.9273855261634 --rfg 17.5833036678754 -i L,0.490505210213802,0.939275152906025 -N 0 -D 3 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1010s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1010s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '6' because it was < 2 characters long 1010s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '12' because it was < 2 characters long 1010s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '14' because it was < 2 characters long 1010s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1010s Warning: skipping read '22' because it was < 2 characters long 1010s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '26' because it was < 2 characters long 1010s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '33' because it was < 2 characters long 1010s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '35' because it was < 2 characters long 1010s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '36' because it was < 2 characters long 1010s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '47' because it was < 2 characters long 1010s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '54' because it was < 2 characters long 1010s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '62' because it was < 2 characters long 1010s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '63' because it was < 2 characters long 1010s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '65' because it was < 2 characters long 1010s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '72' because it was < 2 characters long 1010s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '73' because it was < 2 characters long 1010s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '79' because it was < 2 characters long 1010s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '88' because it was < 2 characters long 1010s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '95' because it was < 2 characters long 1010s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '97' because it was < 2 characters long 1010s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '99' because it was < 2 characters long 1010s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '101' because it was < 2 characters long 1010s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '103' because it was < 2 characters long 1010s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '106' because it was < 2 characters long 1010s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '109' because it was < 2 characters long 1010s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '110' because it was < 2 characters long 1010s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '117' because it was < 2 characters long 1010s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '119' because it was < 2 characters long 1010s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '123' because it was < 2 characters long 1010s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '128' because it was < 2 characters long 1010s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '129' because it was < 2 characters long 1010s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '131' because it was < 2 characters long 1010s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '133' because it was < 2 characters long 1010s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '134' because it was < 2 characters long 1010s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '136' because it was < 2 characters long 1010s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 1010s Warning: skipping read '143' because it was < 2 characters long 1010s 144 reads; of these: 1010s 144 (100.00%) were unpaired; of these: 1010s 144 (100.00%) aligned 0 times 1010s 0 (0.00%) aligned exactly 1 time 1010s 0 (0.00%) aligned >1 times 1010s 0.00% overall alignment rate 1010s Read 50 alignments... 1010s Read 100 alignments... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1010s Processing line... 1011s /usr/bin/bowtie2 --large-index -M 2 --trim3 8 --mp 8.3206353836013,6.04244940476874 --rdg 13.3625473984594,13.3481433655099 --local --cp-ival 2 --mm --cp-min 5 --score-min L,2.19352946497966,6.9273855261634 --rfg 17.5833036678754 -i L,0.490505210213802,0.939275152906025 -N 0 -D 3 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s --- Summary --- 1011s Read 1 reference strings 1011s Checked 0 alignments, 0 edits 1011s --------------- 1011s PASSED 1011s ALSO checking that bowtie2 and bowtie2-align match up 1011s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1011s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '6' because it was < 2 characters long 1011s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '12' because it was < 2 characters long 1011s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '14' because it was < 2 characters long 1011s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1011s Warning: skipping read '22' because it was < 2 characters long 1011s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '26' because it was < 2 characters long 1011s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '33' because it was < 2 characters long 1011s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '35' because it was < 2 characters long 1011s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '36' because it was < 2 characters long 1011s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '47' because it was < 2 characters long 1011s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '54' because it was < 2 characters long 1011s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '62' because it was < 2 characters long 1011s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '63' because it was < 2 characters long 1011s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '65' because it was < 2 characters long 1011s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '72' because it was < 2 characters long 1011s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '73' because it was < 2 characters long 1011s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '79' because it was < 2 characters long 1011s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '88' because it was < 2 characters long 1011s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '95' because it was < 2 characters long 1011s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '97' because it was < 2 characters long 1011s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '99' because it was < 2 characters long 1011s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '101' because it was < 2 characters long 1011s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '103' because it was < 2 characters long 1011s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '106' because it was < 2 characters long 1011s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '109' because it was < 2 characters long 1011s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '110' because it was < 2 characters long 1011s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '117' because it was < 2 characters long 1011s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '119' because it was < 2 characters long 1011s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '123' because it was < 2 characters long 1011s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '128' because it was < 2 characters long 1011s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '129' because it was < 2 characters long 1011s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '131' because it was < 2 characters long 1011s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '133' because it was < 2 characters long 1011s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '134' because it was < 2 characters long 1011s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '136' because it was < 2 characters long 1011s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '143' because it was < 2 characters long 1011s 144 reads; of these: 1011s 144 (100.00%) were unpaired; of these: 1011s 144 (100.00%) aligned 0 times 1011s 0 (0.00%) aligned exactly 1 time 1011s 0 (0.00%) aligned >1 times 1011s 0.00% overall alignment rate 1011s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1011s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1011s /usr/bin/bowtie2 --large-index -M 2 --trim3 8 --mp 8.3206353836013,6.04244940476874 --rdg 13.3625473984594,13.3481433655099 --local --cp-ival 2 --mm --cp-min 5 --score-min L,2.19352946497966,6.9273855261634 --rfg 17.5833036678754 -i L,0.490505210213802,0.939275152906025 -N 0 -D 3 -r -p 4 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1011s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1011s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '6' because it was < 2 characters long 1011s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '12' because it was < 2 characters long 1011s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '14' because it was < 2 characters long 1011s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1011s Warning: skipping read '22' because it was < 2 characters long 1011s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '26' because it was < 2 characters long 1011s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '33' because it was < 2 characters long 1011s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '35' because it was < 2 characters long 1011s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '36' because it was < 2 characters long 1011s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '47' because it was < 2 characters long 1011s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '54' because it was < 2 characters long 1011s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '62' because it was < 2 characters long 1011s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '63' because it was < 2 characters long 1011s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '65' because it was < 2 characters long 1011s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '72' because it was < 2 characters long 1011s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '73' because it was < 2 characters long 1011s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '79' because it was < 2 characters long 1011s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '97' because it was < 2 characters long 1011s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '99' because it was < 2 characters long 1011s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '101' because it was < 2 characters long 1011s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '103' because it was < 2 characters long 1011s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '106' because it was < 2 characters long 1011s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '109' because it was < 2 characters long 1011s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '110' because it was < 2 characters long 1011s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '117' because it was < 2 characters long 1011s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '119' because it was < 2 characters long 1011s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '123' because it was < 2 characters long 1011s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '128' because it was < 2 characters long 1011s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '129' because it was < 2 characters long 1011s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '131' because it was < 2 characters long 1011s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '88' because it was < 2 characters long 1011s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '95' because it was < 2 characters long 1011s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '133' because it was < 2 characters long 1011s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '134' because it was < 2 characters long 1011s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '136' because it was < 2 characters long 1011s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '143' because it was < 2 characters long 1011s 144 reads; of these: 1011s 144 (100.00%) were unpaired; of these: 1011s 144 (100.00%) aligned 0 times 1011s 0 (0.00%) aligned exactly 1 time 1011s 0 (0.00%) aligned >1 times 1011s 0.00% overall alignment rate 1011s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1011s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1011s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1011s Flattened IUPAC characters 1011s Mutating sequence Sim.pm.1 1011s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1011s Finished SNPs 1011s Finished ref gaps 1011s Finished read gaps 1011s Mutating sequence Sim.pm.2 1011s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1011s Finished SNPs 1011s Finished ref gaps 1011s Finished read gaps 1011s Mutated reference genome to subject genome 1011s SNPs introduced: 7 1011s Reference gaps introduced: 0 1011s Read gaps introduced: 1 1011s Rearrangements introduced: 0 1011s Created read sampler 1011s Sampling 75 reads 1011s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1011s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1011s *** Run 23 of 100 1011s /usr/bin/bowtie2 -R 4 --np 2 --score-min L,4.70861916720524,5.15922932724212 --gbar 8 --cp-ival 5 --mm --cp-min 3 --large-index --mp 9.80324020482387,3.35978295448308 --trim3 8 --local -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1011s parsing sequence Sim.pm.1... 1011s parsing sequence Sim.pm.2... 1011s Parsed 81 reference bases 1011s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 1011s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 1011s Warning: skipping mate #1 of read '7' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 1011s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 1011s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 1011s Warning: skipping mate #1 of read '31' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 1011s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1011s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '36' because it was < 2 characters long 1011s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 1011s Warning: skipping mate #2 of read '39' because it was < 2 characters long 1011s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1011s Warning: skipping read '49' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1011s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1011s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1011s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 1011s Warning: skipping mate #2 of read '65' because it was < 2 characters long 1011s Read 50 alignments... 1011s Read 100 alignments... 1011s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 1011s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1011s 75 reads; of these: 1011s 61 (81.33%) were paired; of these: 1011s 61 (100.00%) aligned concordantly 0 times 1011s 0 (0.00%) aligned concordantly exactly 1 time 1011s 0 (0.00%) aligned concordantly >1 times 1011s ---- 1011s 61 pairs aligned concordantly 0 times; of these: 1011s 0 (0.00%) aligned discordantly 1 time 1011s ---- 1011s 61 pairs aligned 0 times concordantly or discordantly; of these: 1011s 122 mates make up the pairs; of these: 1011s 122 (100.00%) aligned 0 times 1011s 0 (0.00%) aligned exactly 1 time 1011s 0 (0.00%) aligned >1 times 1011s 14 (18.67%) were unpaired; of these: 1011s 14 (100.00%) aligned 0 times 1011s 0 (0.00%) aligned exactly 1 time 1011s 0 (0.00%) aligned >1 times 1011s 0.00% overall alignment rate 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s --- Summary --- 1011s Read 1 reference strings 1011s Checked 0 alignments, 0 edits 1011s --------------- 1011s PASSED 1011s Flattened IUPAC characters 1011s Mutating sequence Sim.pm.2 1011s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1011s Finished SNPs 1011s Finished ref gaps 1011s Finished read gaps 1011s Mutating sequence Sim.pm.1 1011s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1011s Finished SNPs 1011s Finished ref gaps 1011s Finished read gaps 1011s Mutated reference genome to subject genome 1011s SNPs introduced: 10 1011s Reference gaps introduced: 1 1011s Read gaps introduced: 0 1011s Rearrangements introduced: 0 1011s Created read sampler 1011s Sampling 40 reads 1011s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1011s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1011s parsing sequence Sim.pm.1... 1011s parsing sequence Sim.pm.2... 1011s Parsed 81 reference bases 1011s *** Run 24 of 100 1011s /usr/bin/bowtie2 -N 1 -L28 --n-ceil 1.0777897197344,0.210873257566349 --score-min L,5.40226481957012,7.42354328092243 --trim5 3 -i C,0.481400748677116,0.372101113027239 --cp-ival 1 --cp-min 6 --large-index --rdg 32.7891030195513 --mp 5.18417566160436,3.59535451680661 --local -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1011s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (1) 1011s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1011s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 1011s Warning: skipping read '18' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 1011s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 1011s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 1011s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1011s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (1) 1011s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1011s 40 reads; of these: 1011s 37 (92.50%) were paired; of these: 1011s 37 (100.00%) aligned concordantly 0 times 1011s 0 (0.00%) aligned concordantly exactly 1 time 1011s 0 (0.00%) aligned concordantly >1 times 1011s ---- 1011s 37 pairs aligned concordantly 0 times; of these: 1011s 0 (0.00%) aligned discordantly 1 time 1011s ---- 1011s 37 pairs aligned 0 times concordantly or discordantly; of these: 1011s 74 mates make up the pairs; of these: 1011s 74 (100.00%) aligned 0 times 1011s 0 (0.00%) aligned exactly 1 time 1011s 0 (0.00%) aligned >1 times 1011s 3 (7.50%) were unpaired; of these: 1011s 3 (100.00%) aligned 0 times 1011s 0 (0.00%) aligned exactly 1 time 1011s 0 (0.00%) aligned >1 times 1011s 0.00% overall alignment rate 1011s Read 50 alignments... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s 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Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s Processing line... 1011s --- Summary --- 1011s Read 1 reference strings 1011s Checked 0 alignments, 0 edits 1011s --------------- 1011s PASSED 1011s ALSO checking that bowtie2 and bowtie2-align match up 1011s /usr/bin/bowtie2 -N 1 -L28 --n-ceil 1.0777897197344,0.210873257566349 --score-min L,5.40226481957012,7.42354328092243 --trim5 3 -i C,0.481400748677116,0.372101113027239 --cp-ival 1 --cp-min 6 --large-index --rdg 32.7891030195513 --mp 5.18417566160436,3.59535451680661 --local -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1012s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (1) 1012s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1012s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 1012s Warning: skipping read '18' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 1012s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 1012s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 1012s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (1) 1012s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1012s 40 reads; of these: 1012s 37 (92.50%) were paired; of these: 1012s 37 (100.00%) aligned concordantly 0 times 1012s 0 (0.00%) aligned concordantly exactly 1 time 1012s 0 (0.00%) aligned concordantly >1 times 1012s ---- 1012s 37 pairs aligned concordantly 0 times; of these: 1012s 0 (0.00%) aligned discordantly 1 time 1012s ---- 1012s 37 pairs aligned 0 times concordantly or discordantly; of these: 1012s 74 mates make up the pairs; of these: 1012s 74 (100.00%) aligned 0 times 1012s 0 (0.00%) aligned exactly 1 time 1012s 0 (0.00%) aligned >1 times 1012s 3 (7.50%) were unpaired; of these: 1012s 3 (100.00%) aligned 0 times 1012s 0 (0.00%) aligned exactly 1 time 1012s 0 (0.00%) aligned >1 times 1012s 0.00% overall alignment rate 1012s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1012s Flattened IUPAC characters 1012s Mutating sequence Sim.pm.1 1012s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1012s Finished SNPs 1012s Finished ref gaps 1012s Finished read gaps 1012s Mutating sequence Sim.pm.2 1012s Introducing 9 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1012s Finished SNPs 1012s Finished ref gaps 1012s Finished read gaps 1012s Mutated reference genome to subject genome 1012s SNPs introduced: 16 1012s Reference gaps introduced: 2 1012s Read gaps introduced: 0 1012s Rearrangements introduced: 0 1012s Created read sampler 1012s Sampling 84 reads 1012s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1012s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1012s parsing sequence Sim.pm.1... 1012s *** Run 25 of 100 1012s /usr/bin/bowtie2 --trim5 6 -i L,0.307387790469435 --rfg 32.2799192787116,12.9076401186871 --n-ceil 0.298048761596039,1.19920303995361 --score-min L,9.46274496351058,7.29741061165924 --norc -N 0 -L16 --rdg 21.0029165145233 --mp 5.21886474760413,3.19024398604908 --local --large-index --cp-min 2 --cp-ival 4 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1012s parsing sequence Sim.pm.2... 1012s Parsed 81 reference bases 1012s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '49' because it was < 2 characters long 1012s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1012s Warning: skipping read '59' because it was < 2 characters long 1012s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #2 of read '61' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1012s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '64' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '65' because it was < 2 characters long 1012s Read 50 alignments... 1012s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '72' because it was < 2 characters long 1012s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #2 of read '76' because it was < 2 characters long 1012s Read 100 alignments... 1012s 84 reads; of these: 1012s 72 (85.71%) were paired; of these: 1012s 72 (100.00%) aligned concordantly 0 times 1012s 0 (0.00%) aligned concordantly exactly 1 time 1012s 0 (0.00%) aligned concordantly >1 times 1012s ---- 1012s 72 pairs aligned concordantly 0 times; of these: 1012s 0 (0.00%) aligned discordantly 1 time 1012s ---- 1012s 72 pairs aligned 0 times concordantly or discordantly; of these: 1012s 144 mates make up the pairs; of these: 1012s 144 (100.00%) aligned 0 times 1012s 0 (0.00%) aligned exactly 1 time 1012s 0 (0.00%) aligned >1 times 1012s 12 (14.29%) were unpaired; of these: 1012s 12 (100.00%) aligned 0 times 1012s 0 (0.00%) aligned exactly 1 time 1012s 0 (0.00%) aligned >1 times 1012s 0.00% overall alignment rate 1012s Read 150 alignments... 1012s Processing line... 1012s Processing line... 1012s /usr/bin/bowtie2 --trim5 6 -i L,0.307387790469435 --rfg 32.2799192787116,12.9076401186871 --n-ceil 0.298048761596039,1.19920303995361 --score-min L,9.46274496351058,7.29741061165924 --norc -N 0 -L16 --rdg 21.0029165145233 --mp 5.21886474760413,3.19024398604908 --local --large-index --cp-min 2 --cp-ival 4 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s 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Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s Processing line... 1012s --- Summary --- 1012s Read 1 reference strings 1012s Checked 0 alignments, 0 edits 1012s --------------- 1012s PASSED 1012s ALSO checking that bowtie2 and bowtie2-align match up 1012s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '49' because it was < 2 characters long 1012s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1012s Warning: skipping read '59' because it was < 2 characters long 1012s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #2 of read '61' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1012s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '64' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '65' because it was < 2 characters long 1012s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '72' because it was < 2 characters long 1012s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #2 of read '76' because it was < 2 characters long 1012s 84 reads; of these: 1012s 72 (85.71%) were paired; of these: 1012s 72 (100.00%) aligned concordantly 0 times 1012s 0 (0.00%) aligned concordantly exactly 1 time 1012s 0 (0.00%) aligned concordantly >1 times 1012s ---- 1012s 72 pairs aligned concordantly 0 times; of these: 1012s 0 (0.00%) aligned discordantly 1 time 1012s ---- 1012s 72 pairs aligned 0 times concordantly or discordantly; of these: 1012s 144 mates make up the pairs; of these: 1012s 144 (100.00%) aligned 0 times 1012s 0 (0.00%) aligned exactly 1 time 1012s 0 (0.00%) aligned >1 times 1012s 12 (14.29%) were unpaired; of these: 1012s 12 (100.00%) aligned 0 times 1012s 0 (0.00%) aligned exactly 1 time 1012s 0 (0.00%) aligned >1 times 1012s 0.00% overall alignment rate 1012s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1012s Flattened IUPAC characters 1012s Mutating sequence Sim.pm.1 1012s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1012s Finished SNPs 1012s Finished ref gaps 1012s Finished read gaps 1012s Mutating sequence Sim.pm.2 1012s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1012s Finished SNPs 1012s Finished ref gaps 1012s Finished read gaps 1012s Mutated reference genome to subject genome 1012s SNPs introduced: 0 1012s Reference gaps introduced: 0 1012s Read gaps introduced: 0 1012s Rearrangements introduced: 0 1012s Created read sampler 1012s Sampling 82 reads 1012s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1012s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1012s parsing sequence Sim.pm.1... 1012s parsing sequence Sim.pm.2... 1012s Parsed 81 reference bases 1012s *** Run 26 of 100 1012s /usr/bin/bowtie2 --trim5 6 --score-min L,1.06827281685695,6.6352876555172 --np 8 --norc -D 14 --mp 6.44159968129172,4.20152575249304 --trim3 6 --rdg 36.2914207413657 --large-index --cp-min 4 --cp-ival 5 --mm -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1012s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1012s Warning: skipping read '3' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1012s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1012s Warning: skipping read '13' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1012s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1012s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '21' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1012s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1012s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1012s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1012s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '31' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1012s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1012s Warning: skipping read '32' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1012s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '33' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1012s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1012s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #2 of read '36' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1012s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '37' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1012s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1012s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1012s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1012s Warning: skipping read '46' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1012s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1012s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1012s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1012s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '54' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1012s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1012s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 1012s Warning: skipping mate #2 of read '58' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1012s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1012s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '64' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1012s Read 50 alignments... 1012s Read 100 alignments... 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1012s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1012s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '75' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1012s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 1012s Warning: skipping mate #1 of read '76' because it was < 2 characters long 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1012s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1012s 82 reads; of these: 1012s 68 (82.93%) were paired; of these: 1012s 68 (100.00%) aligned concordantly 0 times 1012s 0 (0.00%) aligned concordantly exactly 1 time 1012s 0 (0.00%) aligned concordantly >1 times 1012s ---- 1012s 68 pairs aligned concordantly 0 times; of these: 1012s 0 (0.00%) aligned discordantly 1 time 1012s ---- 1012s 68 pairs aligned 0 times concordantly or discordantly; of these: 1012s 136 mates make up the pairs; of these: 1012s 124 (91.18%) aligned 0 times 1012s 3 (2.21%) aligned exactly 1 time 1012s 9 (6.62%) aligned >1 times 1012s 14 (17.07%) were unpaired; of these: 1012s 13 (92.86%) aligned 0 times 1012s 0 (0.00%) aligned exactly 1 time 1012s 1 (7.14%) aligned >1 times 1012s 8.67% overall alignment rate 1012s Read 150 alignments... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GT 1013s GT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AC 1013s AC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AT 1013s AT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GT 1013s GT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AC 1013s AC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s ACAACCG 1013s ACAACCG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GA 1013s GA 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s ATCC 1013s ATCC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AC 1013s AC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s CGT 1013s CGT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AC 1013s AC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s ACAACCGAAAGAC 1013s ACAACCGAAAGAC 1013s Processing line... 1013s Processing line... 1013s TGACAACCGAAAGACGGACGTA 1013s TGACAACCGAAAGACGGACGTA 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s --- Summary --- 1013s Read 1 reference strings 1013s Checked 13 alignments, 0 edits 1013s --------------- 1013s PASSED 1013s Flattened IUPAC characters 1013s Mutating sequence Sim.pm.2 1013s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1013s Finished SNPs 1013s Finished ref gaps 1013s Finished read gaps 1013s Mutating sequence Sim.pm.1 1013s Introducing 9 SNPs, 2/0 ref/read gaps, and 0 rearrangements 1013s Finished SNPs 1013s Finished ref gaps 1013s Finished read gaps 1013s Mutated reference genome to subject genome 1013s SNPs introduced: 13 1013s Reference gaps introduced: 2 1013s Read gaps introduced: 0 1013s Rearrangements introduced: 0 1013s Created read sampler 1013s Sampling 141 reads 1013s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1013s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1013s parsing sequence Sim.pm.1... 1013s parsing sequence Sim.pm.2... 1013s Parsed 81 reference bases 1013s *** Run 27 of 100 1013s /usr/bin/bowtie2 --rfg 13.5287115149854 --mp 5.98806852427583,4.08919992231857 --score-min L,6.94766047901993,8.21444423088234 --n-ceil 0.14506436550546,0.522561175477551 --large-index --ma 13.4728226527525 --norc --np 2 --cp-min 6 --cp-ival 2 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1013s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1013s 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 1013s 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 1013s 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 1013s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (1) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (1) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 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 1013s 141 reads; of these: 1013s 141 (100.00%) were unpaired; of these: 1013s 120 (85.11%) aligned 0 times 1013s 9 (6.38%) aligned exactly 1 time 1013s 12 (8.51%) aligned >1 times 1013s 14.89% overall alignment rate 1013s Read 50 alignments... 1013s Read 100 alignments... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s TATC 1013s TATC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s CCG 1013s CCG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AAGAC 1013s AAGAC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AGACGGACGTA 1013s AGACGGACGTA 1013s Processing line... 1013s Processing line... 1013s TCCCGTATCGCGT 1013s TCCCGTATCGCGT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s TCGC 1013s TCGC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GATGACAACCGA 1013s GATGACAACCGA 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GTA 1013s GTA 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AGA 1013s AGA 1013s Processing line... 1013s CCGAA 1013s CCGAA 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s TCG 1013s TCG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AC 1013s AC 1013s Processing line... 1013s Processing line... 1013s TGACAACCGAAAGACG 1013s TGACAACCGAAAGACG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s TT 1013s TT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GGG 1013s GGG 1013s Processing line... 1013s CGT 1013s CGT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GA 1013s GA 1013s Processing line... 1013s AT 1013s AT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GA 1013s GA 1013s Processing line... 1013s Processing line... 1013s CT 1013s CT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AACCGAAAGACG 1013s AACCGAAAGACG 1013s Processing line... 1013s --- Summary --- 1013s Read 1 reference strings 1013s Checked 21 alignments, 0 edits 1013s --------------- 1013s PASSED 1013s Flattened IUPAC characters 1013s Mutating sequence Sim.pm.2 1013s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1013s Finished SNPs 1013s Finished ref gaps 1013s Finished read gaps 1013s Mutating sequence Sim.pm.1 1013s Introducing 9 SNPs, 1/1 ref/read gaps, and 2 rearrangements 1013s Finished SNPs 1013s Finished ref gaps 1013s Finished read gaps 1013s Mutated reference genome to subject genome 1013s SNPs introduced: 17 1013s Reference gaps introduced: 1 1013s Read gaps introduced: 1 1013s Rearrangements introduced: 2 1013s Created read sampler 1013s Sampling 111 reads 1013s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1013s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1013s parsing sequence Sim.pm.1... 1013s parsing sequence Sim.pm.2... 1013s *** Run 28 of 100 1013s /usr/bin/bowtie2 --cp-min 7 --mm --cp-ival 1 --rdg 35.2504113215417,11.012725409624 --mp 2.3700797029104,1.67001983241722 --large-index --ma 12.2049163376996 --norc -R 1 --trim5 1 --rfg 46.4186893611162,5.984896769615 --score-min L,2.20917931281973,1.88892926441458 -f -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta 1013s Parsed 81 reference bases 1013s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1013s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 1013s Warning: skipping mate #2 of read '17' because it was < 2 characters long 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1013s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 1013s Warning: skipping mate #2 of read '37' because it was < 2 characters long 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1013s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 1013s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1013s Read 50 alignments... 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1013s Read 100 alignments... 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1013s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1013s 111 reads; of these: 1013s 111 (100.00%) were paired; of these: 1013s 109 (98.20%) aligned concordantly 0 times 1013s 0 (0.00%) aligned concordantly exactly 1 time 1013s 2 (1.80%) aligned concordantly >1 times 1013s ---- 1013s 109 pairs aligned concordantly 0 times; of these: 1013s 0 (0.00%) aligned discordantly 1 time 1013s ---- 1013s 109 pairs aligned 0 times concordantly or discordantly; of these: 1013s 218 mates make up the pairs; of these: 1013s 199 (91.28%) aligned 0 times 1013s 8 (3.67%) aligned exactly 1 time 1013s 11 (5.05%) aligned >1 times 1013s 10.36% overall alignment rate 1013s Read 150 alignments... 1013s Read 200 alignments... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GGG 1013s GGG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s TA 1013s TA 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GACGGACGT 1013s GACGGACGT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s CGAAAGACG 1013s CGAAAGACG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s TG 1013s TG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AAAGACGGACG 1013s AAAGACGGACG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s TT 1013s TT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GAAAGAC 1013s GAAAGAC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s CCC 1013s CCC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s ATCCCG 1013s ATCCCG 1013s Processing line... 1013s Processing line... 1013s CGTAG 1013s CGTAG 1013s Processing line... 1013s Processing line... 1013s GT 1013s GT 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AACCGAAAGACGGACGTA 1013s AACCGAAAGACGGACGTA 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s GACG 1013s GACG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s ACCGAAAGACGG 1013s ACCGAAAGACGG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s ATC 1013s ATC 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s AA 1013s AA 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s TAT 1013s TAT 1013s Processing line... 1013s GACG 1013s GACG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s CA 1013s CA 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s CGA 1013s CGA 1013s Processing line... 1013s CG 1013s CG 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s ATCGCGTA 1013s ATCGCGTA 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s --- Summary --- 1013s Read 1 reference strings 1013s Checked 23 alignments, 0 edits 1013s --------------- 1013s PASSED 1013s Flattened IUPAC characters 1013s Mutating sequence Sim.pm.1 1013s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1013s Finished SNPs 1013s Finished ref gaps 1013s Finished read gaps 1013s Mutating sequence Sim.pm.2 1013s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1013s Finished SNPs 1013s Finished ref gaps 1013s Finished read gaps 1013s Mutated reference genome to subject genome 1013s SNPs introduced: 17 1013s Reference gaps introduced: 1 1013s Read gaps introduced: 0 1013s Rearrangements introduced: 0 1013s Created read sampler 1013s Sampling 95 reads 1013s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1013s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1013s *** Run 29 of 100 1013s /usr/bin/bowtie2 --score-min L,4.39498035357023,7.36821726118143 --n-ceil 0.694709835597471,1.37918126966358 --trim5 3 -R 3 --large-index --local -a --rdg 3.89805746373482,8.73875579973415 --cp-ival 1 --cp-min 5 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1013s parsing sequence Sim.pm.1... 1013s parsing sequence Sim.pm.2... 1013s Parsed 81 reference bases 1013s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1013s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1013s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1013s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1013s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 1013s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1013s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1013s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1013s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 1013s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1013s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1013s 95 reads; of these: 1013s 95 (100.00%) were unpaired; of these: 1013s 95 (100.00%) aligned 0 times 1013s 0 (0.00%) aligned exactly 1 time 1013s 0 (0.00%) aligned >1 times 1013s 0.00% overall alignment rate 1013s Read 50 alignments... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s Processing line... 1013s --- Summary --- 1013s Read 1 reference strings 1013s Checked 0 alignments, 0 edits 1013s --------------- 1013s PASSED 1013s Flattened IUPAC characters 1013s Mutating sequence Sim.pm.2 1013s Introducing 11 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1013s Finished SNPs 1013s Finished ref gaps 1013s Finished read gaps 1013s Mutating sequence Sim.pm.1 1013s Introducing 8 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1013s Finished SNPs 1013s Finished ref gaps 1013s Finished read gaps 1013s Mutated reference genome to subject genome 1013s SNPs introduced: 19 1013s Reference gaps introduced: 0 1013s Read gaps introduced: 2 1013s Rearrangements introduced: 0 1013s Created read sampler 1013s Sampling 72 reads 1013s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1013s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1013s parsing sequence Sim.pm.1... 1013s parsing sequence Sim.pm.2... 1013s Parsed 81 reference bases 1013s *** Run 30 of 100 1013s /usr/bin/bowtie2 --gbar 1 --score-min L,9.27593355740158,6.05392449469473 --large-index --ma 37.432282074701 --rfg 45.5579288534 --rdg 13.9735486934668 --trim5 2 --trim3 5 --cp-ival 1 --np 2 --cp-min 3 --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq 1014s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 1014s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #2 of read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 1014s Warning: skipping mate #2 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Read 50 alignments... 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 72 reads; of these: 1014s 61 (84.72%) were paired; of these: 1014s 61 (100.00%) aligned concordantly 0 times 1014s 0 (0.00%) aligned concordantly exactly 1 time 1014s 0 (0.00%) aligned concordantly >1 times 1014s ---- 1014s 61 pairs aligned concordantly 0 times; of these: 1014s 0 (0.00%) aligned discordantly 1 time 1014s ---- 1014s 61 pairs aligned 0 times concordantly or discordantly; of these: 1014s 122 mates make up the pairs; of these: 1014s 108 (88.52%) aligned 0 times 1014s 8 (6.56%) aligned exactly 1 time 1014s 6 (4.92%) aligned >1 times 1014s 11 (15.28%) were unpaired; of these: 1014s 11 (100.00%) aligned 0 times 1014s 0 (0.00%) aligned exactly 1 time 1014s 0 (0.00%) aligned >1 times 1014s 10.53% overall alignment rate 1014s Read 100 alignments... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s TC 1014s TC 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s TATCGCGTA 1014s TATCGCGTA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s GA 1014s GA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s TCAC 1014s TCAC 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s CCGT 1014s CCGT 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s GACAACCGAAA 1014s GACAACCGAAA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s ACAACCGAAAGACGGAC 1014s ACAACCGAAAGACGGAC 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s ACAA 1014s ACAA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s GA 1014s GA 1014s Processing line... 1014s Processing line... 1014s AAG 1014s AAG 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s GACA 1014s GACA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s ATCCCGTA 1014s ATCCCGTA 1014s Processing line... 1014s Processing line... 1014s CCGAAA 1014s CCGAAA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s AGACGGA 1014s AGACGGA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s --- Summary --- 1014s Read 1 reference strings 1014s Checked 14 alignments, 0 edits 1014s --------------- 1014s /usr/bin/bowtie2 --gbar 1 --score-min L,9.27593355740158,6.05392449469473 --large-index --ma 37.432282074701 --rfg 45.5579288534 --rdg 13.9735486934668 --trim5 2 --trim3 5 --cp-ival 1 --np 2 --cp-min 3 --qseq -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1014s PASSED 1014s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1014s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #2 of read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 1014s Warning: skipping mate #2 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 1014s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 1014s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 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 1014s 72 reads; of these: 1014s 61 (84.72%) were paired; of these: 1014s 61 (100.00%) aligned concordantly 0 times 1014s 0 (0.00%) aligned concordantly exactly 1 time 1014s 0 (0.00%) aligned concordantly >1 times 1014s ---- 1014s 61 pairs aligned concordantly 0 times; of these: 1014s 0 (0.00%) aligned discordantly 1 time 1014s ---- 1014s 61 pairs aligned 0 times concordantly or discordantly; of these: 1014s 122 mates make up the pairs; of these: 1014s 108 (88.52%) aligned 0 times 1014s 8 (6.56%) aligned exactly 1 time 1014s 6 (4.92%) aligned >1 times 1014s 11 (15.28%) were unpaired; of these: 1014s 11 (100.00%) aligned 0 times 1014s 0 (0.00%) aligned exactly 1 time 1014s 0 (0.00%) aligned >1 times 1014s 10.53% overall alignment rate 1014s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1014s Flattened IUPAC characters 1014s Mutating sequence Sim.pm.1 1014s Introducing 0 SNPs, 2/2 ref/read gaps, and 0 rearrangements 1014s Finished SNPs 1014s Finished ref gaps 1014s Finished read gaps 1014s Mutating sequence Sim.pm.2 1014s Introducing 7 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1014s Finished SNPs 1014s Finished ref gaps 1014s Finished read gaps 1014s Mutated reference genome to subject genome 1014s SNPs introduced: 7 1014s Reference gaps introduced: 2 1014s Read gaps introduced: 4 1014s Rearrangements introduced: 0 1014s Created read sampler 1014s Sampling 148 reads 1014s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1014s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1014s parsing sequence Sim.pm.1... 1014s parsing sequence Sim.pm.2... 1014s *** Run 31 of 100 1014s /usr/bin/bowtie2 --score-min L,1.52350228163306,1.85144061845376 --rfg 16.8661582281922 --trim5 2 --np 1 --large-index --local --mp 4.4477967475833,1.17972896586962 --rdg 2.18083536129957,13.1964340213206 --cp-ival 1 --cp-min 5 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1014s Parsed 81 reference bases 1014s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '1' because it was < 2 characters long 1014s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '2' because it was < 2 characters long 1014s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '4' because it was < 2 characters long 1014s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '8' because it was < 2 characters long 1014s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read '12' because it was < 2 characters long 1014s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '14' because it was < 2 characters long 1014s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '19' because it was < 2 characters long 1014s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read '24' because it was < 2 characters long 1014s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '30' because it was < 2 characters long 1014s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read '32' because it was < 2 characters long 1014s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '38' because it was < 2 characters long 1014s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '49' because it was < 2 characters long 1014s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '62' because it was < 2 characters long 1014s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read '64' because it was < 2 characters long 1014s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '69' because it was < 2 characters long 1014s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read '85' because it was < 2 characters long 1014s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read '91' because it was < 2 characters long 1014s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read '93' because it was < 2 characters long 1014s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read '126' because it was < 2 characters long 1014s Warning: skipping read '139' because length (1) <= # seed mismatches (0) 1014s Warning: skipping read '139' because it was < 2 characters long 1014s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 1014s Warning: skipping read '146' because it was < 2 characters long 1014s 148 reads; of these: 1014s 148 (100.00%) were unpaired; of these: 1014s 134 (90.54%) aligned 0 times 1014s 11 (7.43%) aligned exactly 1 time 1014s 3 (2.03%) aligned >1 times 1014s 9.46% overall alignment rate 1014s Read 50 alignments... 1014s Read 100 alignments... 1014s Read 150 alignments... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s GACG 1014s GACG 1014s Processing line... 1014s AAGACGGACGTA 1014s AAGACGGACGTA 1014s Processing line... 1014s Processing line... 1014s CGTATCGCGTAGTGATGACAACCGAAAGACGGACG 1014s CGTATCGCGTAGNGATGACAACCGAAAGACGGACG 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s CACGTGGGC 1014s CACGTGGGC 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s GTATCGCG 1014s GTATCGCG 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s CCGAAAGACG 1014s CCGAAAGACG 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s CGAA 1014s CGAA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s GATGACA 1014s GATGACA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s ATGACAACCGAAAGACGGACGTA 1014s ATGACAACCGAAAGACGGACGTA 1014s Processing line... 1014s Processing line... 1014s AAGACGGACGTA 1014s AAGACGGACGTA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s ACGTGGGCGAC 1014s ACGTGGGCGAC 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s ATGACAACCGAAAGACGGACGTACATCCCGTATCGCGTAG 1014s ATGACAACCGAAAGACGGACGTANATCCCGTATCGCGTAG 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s ATGA 1014s ATGA 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s Processing line... 1014s CCGT 1014s CCGT 1014s /usr/bin/bowtie2 --score-min L,1.52350228163306,1.85144061845376 --rfg 16.8661582281922 --trim5 2 --np 1 --large-index --local --mp 4.4477967475833,1.17972896586962 --rdg 2.18083536129957,13.1964340213206 --cp-ival 1 --cp-min 5 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1014s --- Summary --- 1014s Read 1 reference strings 1014s Checked 14 alignments, 0 edits 1014s --------------- 1014s PASSED 1014s ALSO checking that bowtie2 and bowtie2-align match up 1015s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '1' because it was < 2 characters long 1015s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '2' because it was < 2 characters long 1015s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '4' because it was < 2 characters long 1015s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '8' because it was < 2 characters long 1015s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '12' because it was < 2 characters long 1015s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '14' because it was < 2 characters long 1015s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '19' because it was < 2 characters long 1015s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '24' because it was < 2 characters long 1015s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '30' because it was < 2 characters long 1015s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '32' because it was < 2 characters long 1015s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '38' because it was < 2 characters long 1015s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '49' because it was < 2 characters long 1015s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '62' because it was < 2 characters long 1015s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '64' because it was < 2 characters long 1015s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '69' because it was < 2 characters long 1015s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '85' because it was < 2 characters long 1015s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '91' because it was < 2 characters long 1015s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '93' because it was < 2 characters long 1015s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '126' because it was < 2 characters long 1015s Warning: skipping read '139' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '139' because it was < 2 characters long 1015s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '146' because it was < 2 characters long 1015s 148 reads; of these: 1015s 148 (100.00%) were unpaired; of these: 1015s 134 (90.54%) aligned 0 times 1015s 11 (7.43%) aligned exactly 1 time 1015s 3 (2.03%) aligned >1 times 1015s 9.46% overall alignment rate 1015s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1015s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1015s /usr/bin/bowtie2 --score-min L,1.52350228163306,1.85144061845376 --rfg 16.8661582281922 --trim5 2 --np 1 --large-index --local --mp 4.4477967475833,1.17972896586962 --rdg 2.18083536129957,13.1964340213206 --cp-ival 1 --cp-min 5 -q -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1015s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '1' because it was < 2 characters long 1015s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '2' because it was < 2 characters long 1015s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '4' because it was < 2 characters long 1015s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '8' because it was < 2 characters long 1015s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '12' because it was < 2 characters long 1015s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '14' because it was < 2 characters long 1015s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '19' because it was < 2 characters long 1015s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '24' because it was < 2 characters long 1015s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '30' because it was < 2 characters long 1015s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '32' because it was < 2 characters long 1015s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '49' because it was < 2 characters long 1015s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '62' because it was < 2 characters long 1015s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '64' because it was < 2 characters long 1015s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '69' because it was < 2 characters long 1015s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '38' because it was < 2 characters long 1015s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '126' because it was < 2 characters long 1015s Warning: skipping read '139' because length (1) <= # seed mismatches (0) 1015s Warning: skipping read '139' because it was < 2 characters long 1015s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '85' because it was < 2 characters long 1015s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '146' because it was < 2 characters long 1015s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '91' because it was < 2 characters long 1015s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1015s Warning: skipping read '93' because it was < 2 characters long 1015s 148 reads; of these: 1015s 148 (100.00%) were unpaired; of these: 1015s 134 (90.54%) aligned 0 times 1015s 11 (7.43%) aligned exactly 1 time 1015s 3 (2.03%) aligned >1 times 1015s 9.46% overall alignment rate 1015s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1015s Flattened IUPAC characters 1015s Mutating sequence Sim.pm.2 1015s Introducing 8 SNPs, 0/1 ref/read gaps, and 3 rearrangements 1015s Finished SNPs 1015s Finished ref gaps 1015s Finished read gaps 1015s Mutating sequence Sim.pm.1 1015s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1015s Finished SNPs 1015s Finished ref gaps 1015s Finished read gaps 1015s Mutated reference genome to subject genome 1015s SNPs introduced: 13 1015s Reference gaps introduced: 0 1015s Read gaps introduced: 1 1015s Rearrangements introduced: 3 1015s Created read sampler 1015s Sampling 21 reads 1015s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1015s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1015s parsing sequence Sim.pm.1... 1015s parsing sequence Sim.pm.2... 1015s Parsed 81 reference bases 1015s *** Run 32 of 100 1015s /usr/bin/bowtie2 --trim5 5 --rfg 35.5062874923621 --score-min L,9.24807205148327,5.48839137587383 -R 3 --rdg 28.5814865172963 --trim3 1 --mp 2.04059250766894,1.31022103799916 --large-index --ma 15.7778138095113 --cp-min 5 --mm --cp-ival 2 --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq 1015s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1015s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1015s 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 1015s 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 1015s 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 1015s 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 1015s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1015s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1015s 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 1015s 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 1015s 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 1015s 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 1015s Warning: skipping mate #2 of read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 1015s Warning: skipping mate #2 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1015s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 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 1015s 21 reads; of these: 1015s 20 (95.24%) were paired; of these: 1015s 20 (100.00%) aligned concordantly 0 times 1015s 0 (0.00%) aligned concordantly exactly 1 time 1015s 0 (0.00%) aligned concordantly >1 times 1015s ---- 1015s 20 pairs aligned concordantly 0 times; of these: 1015s 0 (0.00%) aligned discordantly 1 time 1015s ---- 1015s 20 pairs aligned 0 times concordantly or discordantly; of these: 1015s 40 mates make up the pairs; of these: 1015s 36 (90.00%) aligned 0 times 1015s 3 (7.50%) aligned exactly 1 time 1015s 1 (2.50%) aligned >1 times 1015s 1 (4.76%) were unpaired; of these: 1015s 0 (0.00%) aligned 0 times 1015s 1 (100.00%) aligned exactly 1 time 1015s 0 (0.00%) aligned >1 times 1015s 12.20% overall alignment rate 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s TGACAACCGA 1015s TGACAACCGA 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s GACGGACGT 1015s GACGGACGT 1015s Processing line... 1015s Processing line... 1015s ACGGACGT 1015s ACGGACGT 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s AAGACGGAC 1015s AAGACGGAC 1015s Processing line... 1015s CG 1015s CG 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s Processing line... 1015s --- Summary --- 1015s Read 1 reference strings 1015s Checked 5 alignments, 0 edits 1015s --------------- 1015s PASSED 1015s Flattened IUPAC characters 1015s Mutating sequence Sim.pm.1 1015s Introducing 4 SNPs, 2/0 ref/read gaps, and 0 rearrangements 1015s Finished SNPs 1015s Finished ref gaps 1015s Finished read gaps 1015s Mutating sequence Sim.pm.2 1015s Introducing 4 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1015s Finished SNPs 1015s Finished ref gaps 1015s Finished read gaps 1015s Mutated reference genome to subject genome 1015s SNPs introduced: 8 1015s Reference gaps introduced: 2 1015s Read gaps introduced: 2 1015s Rearrangements introduced: 0 1015s Created read sampler 1015s Sampling 86 reads 1015s *** Run 33 of 100 1015s /usr/bin/bowtie2 --score-min L,8.38550298091385,4.34607035406678 --norc --local --mp 4.80377028850861,1.4629788488863 --trim3 1 -a --rdg 9.25269206356203 --large-index --cp-min 5 --cp-ival 1 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1015s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1015s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1015s parsing sequence Sim.pm.1... 1015s parsing sequence Sim.pm.2... 1015s Parsed 81 reference bases 1016s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1016s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1016s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1016s Read 50 alignments... 1016s Read 100 alignments... 1016s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #2 of read '75' because it was < 2 characters long 1016s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #2 of read '83' because it was < 2 characters long 1016s 86 reads; of these: 1016s 84 (97.67%) were paired; of these: 1016s 84 (100.00%) aligned concordantly 0 times 1016s 0 (0.00%) aligned concordantly exactly 1 time 1016s 0 (0.00%) aligned concordantly >1 times 1016s ---- 1016s 84 pairs aligned concordantly 0 times; of these: 1016s 0 (0.00%) aligned discordantly 1 time 1016s ---- 1016s 84 pairs aligned 0 times concordantly or discordantly; of these: 1016s 168 mates make up the pairs; of these: 1016s 168 (100.00%) aligned 0 times 1016s 0 (0.00%) aligned exactly 1 time 1016s 0 (0.00%) aligned >1 times 1016s 2 (2.33%) were unpaired; of these: 1016s 2 (100.00%) aligned 0 times 1016s 0 (0.00%) aligned exactly 1 time 1016s 0 (0.00%) aligned >1 times 1016s 0.00% overall alignment rate 1016s Read 150 alignments... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s --- Summary --- 1016s Read 1 reference strings 1016s Checked 0 alignments, 0 edits 1016s --------------- 1016s PASSED 1016s /usr/bin/bowtie2 --score-min L,8.38550298091385,4.34607035406678 --norc --local --mp 4.80377028850861,1.4629788488863 --trim3 1 -a --rdg 9.25269206356203 --large-index --cp-min 5 --cp-ival 1 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1016s ALSO checking that bowtie2 and bowtie2-align match up 1016s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1016s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1016s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1016s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #2 of read '75' because it was < 2 characters long 1016s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #2 of read '83' because it was < 2 characters long 1016s 86 reads; of these: 1016s 84 (97.67%) were paired; of these: 1016s 84 (100.00%) aligned concordantly 0 times 1016s 0 (0.00%) aligned concordantly exactly 1 time 1016s 0 (0.00%) aligned concordantly >1 times 1016s ---- 1016s 84 pairs aligned concordantly 0 times; of these: 1016s 0 (0.00%) aligned discordantly 1 time 1016s ---- 1016s 84 pairs aligned 0 times concordantly or discordantly; of these: 1016s 168 mates make up the pairs; of these: 1016s 168 (100.00%) aligned 0 times 1016s 0 (0.00%) aligned exactly 1 time 1016s 0 (0.00%) aligned >1 times 1016s 2 (2.33%) were unpaired; of these: 1016s 2 (100.00%) aligned 0 times 1016s 0 (0.00%) aligned exactly 1 time 1016s 0 (0.00%) aligned >1 times 1016s 0.00% overall alignment rate 1016s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1016s Flattened IUPAC characters 1016s Mutating sequence Sim.pm.1 1016s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1016s Finished SNPs 1016s Finished ref gaps 1016s Finished read gaps 1016s Mutating sequence Sim.pm.2 1016s Introducing 8 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1016s Finished SNPs 1016s Finished ref gaps 1016s Finished read gaps 1016s Mutated reference genome to subject genome 1016s SNPs introduced: 11 1016s Reference gaps introduced: 2 1016s Read gaps introduced: 1 1016s Rearrangements introduced: 0 1016s Created read sampler 1016s Sampling 42 reads 1016s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1016s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1016s *** Run 34 of 100 1016s /usr/bin/bowtie2 -R 1 --trim5 2 --score-min L,1.44402890733558,5.22325587178429 --gbar 1 --n-ceil 0.481361379574853,0.257671605517197 --cp-min 3 --cp-ival 2 --local -a --mp 5.7995877615013,5.581394588304 --rdg 17.2375948299633 --large-index -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1016s parsing sequence Sim.pm.1... 1016s parsing sequence Sim.pm.2... 1016s Parsed 81 reference bases 1016s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1016s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1016s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #2 of read '39' because it was < 2 characters long 1016s 42 reads; of these: 1016s 41 (97.62%) were paired; of these: 1016s 41 (100.00%) aligned concordantly 0 times 1016s 0 (0.00%) aligned concordantly exactly 1 time 1016s 0 (0.00%) aligned concordantly >1 times 1016s ---- 1016s 41 pairs aligned concordantly 0 times; of these: 1016s 0 (0.00%) aligned discordantly 1 time 1016s ---- 1016s 41 pairs aligned 0 times concordantly or discordantly; of these: 1016s 82 mates make up the pairs; of these: 1016s 82 (100.00%) aligned 0 times 1016s 0 (0.00%) aligned exactly 1 time 1016s 0 (0.00%) aligned >1 times 1016s 1 (2.38%) were unpaired; of these: 1016s 1 (100.00%) aligned 0 times 1016s 0 (0.00%) aligned exactly 1 time 1016s 0 (0.00%) aligned >1 times 1016s 0.00% overall alignment rate 1016s Read 50 alignments... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s /usr/bin/bowtie2 -R 1 --trim5 2 --score-min L,1.44402890733558,5.22325587178429 --gbar 1 --n-ceil 0.481361379574853,0.257671605517197 --cp-min 3 --cp-ival 2 --local -a --mp 5.7995877615013,5.581394588304 --rdg 17.2375948299633 --large-index -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s Processing line... 1016s --- Summary --- 1016s Read 1 reference strings 1016s Checked 0 alignments, 0 edits 1016s --------------- 1016s PASSED 1016s ALSO checking that bowtie2 and bowtie2-align match up 1016s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1016s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1016s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 1016s Warning: skipping mate #2 of read '39' because it was < 2 characters long 1017s 42 reads; of these: 1017s 41 (97.62%) were paired; of these: 1017s 41 (100.00%) aligned concordantly 0 times 1017s 0 (0.00%) aligned concordantly exactly 1 time 1017s 0 (0.00%) aligned concordantly >1 times 1017s ---- 1017s 41 pairs aligned concordantly 0 times; of these: 1017s 0 (0.00%) aligned discordantly 1 time 1017s ---- 1017s 41 pairs aligned 0 times concordantly or discordantly; of these: 1017s 82 mates make up the pairs; of these: 1017s 82 (100.00%) aligned 0 times 1017s 0 (0.00%) aligned exactly 1 time 1017s 0 (0.00%) aligned >1 times 1017s 1 (2.38%) were unpaired; of these: 1017s 1 (100.00%) aligned 0 times 1017s 0 (0.00%) aligned exactly 1 time 1017s 0 (0.00%) aligned >1 times 1017s 0.00% overall alignment rate 1017s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1017s Flattened IUPAC characters 1017s Mutating sequence Sim.pm.1 1017s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1017s Finished SNPs 1017s Finished ref gaps 1017s Finished read gaps 1017s Mutating sequence Sim.pm.2 1017s Introducing 11 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1017s Finished SNPs 1017s Finished ref gaps 1017s Finished read gaps 1017s Mutated reference genome to subject genome 1017s SNPs introduced: 14 1017s Reference gaps introduced: 0 1017s Read gaps introduced: 1 1017s Rearrangements introduced: 1 1017s Created read sampler 1017s Sampling 115 reads 1017s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1017s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1017s parsing sequence Sim.pm.1... 1017s parsing sequence Sim.pm.2... 1017s Parsed 81 reference bases 1017s *** Run 35 of 100 1017s /usr/bin/bowtie2 --np 1 --nofw --trim5 4 --rfg 14.390578461438,6.78272523616052 --score-min L,7.49190722164331,4.54842484351998 --gbar 3 --cp-min 3 --cp-ival 1 --mm --mp 5.82890742945351,4.01571127741386 -a --trim3 9 --rdg 25.0797078110162,18.3120549323618 --local --large-index -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1017s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '2' because it was < 2 characters long 1017s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '6' because it was < 2 characters long 1017s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '8' because it was < 2 characters long 1017s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '12' because it was < 2 characters long 1017s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '13' because it was < 2 characters long 1017s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '14' because it was < 2 characters long 1017s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '20' because it was < 2 characters long 1017s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '21' because it was < 2 characters long 1017s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '23' because it was < 2 characters long 1017s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 1017s Warning: skipping read '25' because it was < 2 characters long 1017s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '26' because it was < 2 characters long 1017s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '29' because it was < 2 characters long 1017s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '30' because it was < 2 characters long 1017s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '34' because it was < 2 characters long 1017s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '36' because it was < 2 characters long 1017s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '37' because it was < 2 characters long 1017s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '40' because it was < 2 characters long 1017s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '41' because it was < 2 characters long 1017s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '42' because it was < 2 characters long 1017s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '43' because it was < 2 characters long 1017s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '45' because it was < 2 characters long 1017s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '46' because it was < 2 characters long 1017s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '54' because it was < 2 characters long 1017s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '59' because it was < 2 characters long 1017s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '61' because it was < 2 characters long 1017s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 1017s Warning: skipping read '62' because it was < 2 characters long 1017s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '69' because it was < 2 characters long 1017s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '71' because it was < 2 characters long 1017s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '73' because it was < 2 characters long 1017s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '79' because it was < 2 characters long 1017s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '80' because it was < 2 characters long 1017s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '81' because it was < 2 characters long 1017s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '84' because it was < 2 characters long 1017s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '86' because it was < 2 characters long 1017s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 1017s Warning: skipping read '88' because it was < 2 characters long 1017s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '92' because it was < 2 characters long 1017s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 1017s Warning: skipping read '94' because it was < 2 characters long 1017s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '99' because it was < 2 characters long 1017s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '101' because it was < 2 characters long 1017s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '102' because it was < 2 characters long 1017s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '103' because it was < 2 characters long 1017s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '106' because it was < 2 characters long 1017s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '110' because it was < 2 characters long 1017s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '114' because it was < 2 characters long 1017s 115 reads; of these: 1017s 115 (100.00%) were unpaired; of these: 1017s 115 (100.00%) aligned 0 times 1017s 0 (0.00%) aligned exactly 1 time 1017s 0 (0.00%) aligned >1 times 1017s 0.00% overall alignment rate 1017s Read 50 alignments... 1017s Read 100 alignments... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s /usr/bin/bowtie2 --np 1 --nofw --trim5 4 --rfg 14.390578461438,6.78272523616052 --score-min L,7.49190722164331,4.54842484351998 --gbar 3 --cp-min 3 --cp-ival 1 --mm --mp 5.82890742945351,4.01571127741386 -a --trim3 9 --rdg 25.0797078110162,18.3120549323618 --local --large-index -r -p 3 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s --- Summary --- 1017s Read 1 reference strings 1017s Checked 0 alignments, 0 edits 1017s --------------- 1017s PASSED 1017s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1017s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '2' because it was < 2 characters long 1017s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '6' because it was < 2 characters long 1017s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '8' because it was < 2 characters long 1017s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '12' because it was < 2 characters long 1017s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '13' because it was < 2 characters long 1017s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '14' because it was < 2 characters long 1017s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '20' because it was < 2 characters long 1017s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '21' because it was < 2 characters long 1017s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '23' because it was < 2 characters long 1017s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 1017s Warning: skipping read '25' because it was < 2 characters long 1017s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '26' because it was < 2 characters long 1017s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '29' because it was < 2 characters long 1017s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '30' because it was < 2 characters long 1017s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '34' because it was < 2 characters long 1017s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '36' because it was < 2 characters long 1017s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '37' because it was < 2 characters long 1017s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '40' because it was < 2 characters long 1017s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '41' because it was < 2 characters long 1017s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '42' because it was < 2 characters long 1017s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '43' because it was < 2 characters long 1017s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '45' because it was < 2 characters long 1017s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '46' because it was < 2 characters long 1017s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '69' because it was < 2 characters long 1017s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '71' because it was < 2 characters long 1017s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '73' because it was < 2 characters long 1017s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '79' because it was < 2 characters long 1017s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '80' because it was < 2 characters long 1017s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '81' because it was < 2 characters long 1017s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '84' because it was < 2 characters long 1017s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '86' because it was < 2 characters long 1017s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 1017s Warning: skipping read '88' because it was < 2 characters long 1017s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '54' because it was < 2 characters long 1017s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '59' because it was < 2 characters long 1017s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '61' because it was < 2 characters long 1017s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 1017s Warning: skipping read '62' because it was < 2 characters long 1017s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '99' because it was < 2 characters long 1017s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '101' because it was < 2 characters long 1017s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '102' because it was < 2 characters long 1017s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '103' because it was < 2 characters long 1017s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '106' because it was < 2 characters long 1017s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '110' because it was < 2 characters long 1017s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '114' because it was < 2 characters long 1017s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1017s Warning: skipping read '92' because it was < 2 characters long 1017s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 1017s Warning: skipping read '94' because it was < 2 characters long 1017s 115 reads; of these: 1017s 115 (100.00%) were unpaired; of these: 1017s 115 (100.00%) aligned 0 times 1017s 0 (0.00%) aligned exactly 1 time 1017s 0 (0.00%) aligned >1 times 1017s 0.00% overall alignment rate 1017s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1017s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1017s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1017s Flattened IUPAC characters 1017s Mutating sequence Sim.pm.2 1017s Introducing 6 SNPs, 2/2 ref/read gaps, and 0 rearrangements 1017s Finished SNPs 1017s Finished ref gaps 1017s Finished read gaps 1017s Mutating sequence Sim.pm.1 1017s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1017s Finished SNPs 1017s Finished ref gaps 1017s Finished read gaps 1017s Mutated reference genome to subject genome 1017s SNPs introduced: 10 1017s Reference gaps introduced: 3 1017s Read gaps introduced: 2 1017s Rearrangements introduced: 1 1017s Created read sampler 1017s Sampling 112 reads 1017s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1017s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1017s parsing sequence Sim.pm.1... 1017s parsing sequence Sim.pm.2... 1017s *** Run 36 of 100 1017s /usr/bin/bowtie2 --cp-min 4 --cp-ival 2 --mm --trim3 1 --mp 4.44628505452267,3.44821216217151 -a --rdg 7.59202202983288 --local --large-index --np 3 -i S,2.48095216224014,3.35422404720869 --rfg 40.5323092854797,12.2434820591919 --score-min L,7.46224335920563,6.63572734083833 --gbar 2 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1017s Parsed 81 reference bases 1017s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1017s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1017s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1017s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1017s Read 50 alignments... 1017s Read 100 alignments... 1017s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1017s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1017s 112 reads; of these: 1017s 111 (99.11%) were paired; of these: 1017s 111 (100.00%) aligned concordantly 0 times 1017s 0 (0.00%) aligned concordantly exactly 1 time 1017s 0 (0.00%) aligned concordantly >1 times 1017s ---- 1017s 111 pairs aligned concordantly 0 times; of these: 1017s 0 (0.00%) aligned discordantly 1 time 1017s ---- 1017s 111 pairs aligned 0 times concordantly or discordantly; of these: 1017s 222 mates make up the pairs; of these: 1017s 222 (100.00%) aligned 0 times 1017s 0 (0.00%) aligned exactly 1 time 1017s 0 (0.00%) aligned >1 times 1017s 1 (0.89%) were unpaired; of these: 1017s 1 (100.00%) aligned 0 times 1017s 0 (0.00%) aligned exactly 1 time 1017s 0 (0.00%) aligned >1 times 1017s 0.00% overall alignment rate 1017s Read 150 alignments... 1017s Read 200 alignments... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s /usr/bin/bowtie2 --cp-min 4 --cp-ival 2 --mm --trim3 1 --mp 4.44628505452267,3.44821216217151 -a --rdg 7.59202202983288 --local --large-index --np 3 -i S,2.48095216224014,3.35422404720869 --rfg 40.5323092854797,12.2434820591919 --score-min L,7.46224335920563,6.63572734083833 --gbar 2 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s Processing line... 1017s --- Summary --- 1017s Read 1 reference strings 1017s Checked 0 alignments, 0 edits 1017s --------------- 1017s PASSED 1017s ALSO checking that bowtie2 and bowtie2-align match up 1018s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1018s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1018s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1018s 112 reads; of these: 1018s 111 (99.11%) were paired; of these: 1018s 111 (100.00%) aligned concordantly 0 times 1018s 0 (0.00%) aligned concordantly exactly 1 time 1018s 0 (0.00%) aligned concordantly >1 times 1018s ---- 1018s 111 pairs aligned concordantly 0 times; of these: 1018s 0 (0.00%) aligned discordantly 1 time 1018s ---- 1018s 111 pairs aligned 0 times concordantly or discordantly; of these: 1018s 222 mates make up the pairs; of these: 1018s 222 (100.00%) aligned 0 times 1018s 0 (0.00%) aligned exactly 1 time 1018s 0 (0.00%) aligned >1 times 1018s 1 (0.89%) were unpaired; of these: 1018s 1 (100.00%) aligned 0 times 1018s 0 (0.00%) aligned exactly 1 time 1018s 0 (0.00%) aligned >1 times 1018s 0.00% overall alignment rate 1018s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1018s Flattened IUPAC characters 1018s Mutating sequence Sim.pm.2 1018s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1018s Finished SNPs 1018s Finished ref gaps 1018s Finished read gaps 1018s Mutating sequence Sim.pm.1 1018s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1018s Finished SNPs 1018s Finished ref gaps 1018s Finished read gaps 1018s Mutated reference genome to subject genome 1018s SNPs introduced: 13 1018s Reference gaps introduced: 0 1018s Read gaps introduced: 1 1018s Rearrangements introduced: 1 1018s Created read sampler 1018s Sampling 25 reads 1018s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1018s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1018s parsing sequence Sim.pm.1... 1018s parsing sequence Sim.pm.2... 1018s *** Run 37 of 100 1018s /usr/bin/bowtie2 --score-min L,9.2901161781791,1.07755356216433 --norc --nofw --np 1 --large-index --ma 27.7450698266416 -M 5 --mp 6.63663010537325,2.94654559830966 --mm --cp-ival 1 --cp-min 3 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1018s Parsed 81 reference bases 1018s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1018s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1018s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1018s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1018s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1018s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1018s 25 reads; of these: 1018s 25 (100.00%) were paired; of these: 1018s 25 (100.00%) aligned concordantly 0 times 1018s 0 (0.00%) aligned concordantly exactly 1 time 1018s 0 (0.00%) aligned concordantly >1 times 1018s ---- 1018s 25 pairs aligned concordantly 0 times; of these: 1018s 0 (0.00%) aligned discordantly 1 time 1018s ---- 1018s 25 pairs aligned 0 times concordantly or discordantly; of these: 1018s 50 mates make up the pairs; of these: 1018s 50 (100.00%) aligned 0 times 1018s 0 (0.00%) aligned exactly 1 time 1018s 0 (0.00%) aligned >1 times 1018s 0.00% overall alignment rate 1018s Read 50 alignments... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s --- Summary --- 1018s Read 1 reference strings 1018s Checked 0 alignments, 0 edits 1018s --------------- 1018s PASSED 1018s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1018s /usr/bin/bowtie2 --score-min L,9.2901161781791,1.07755356216433 --norc --nofw --np 1 --large-index --ma 27.7450698266416 -M 5 --mp 6.63663010537325,2.94654559830966 --mm --cp-ival 1 --cp-min 3 -q -p 3 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1018s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1018s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1018s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1018s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1018s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1018s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1018s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1018s 25 reads; of these: 1018s 25 (100.00%) were paired; of these: 1018s 25 (100.00%) aligned concordantly 0 times 1018s 0 (0.00%) aligned concordantly exactly 1 time 1018s 0 (0.00%) aligned concordantly >1 times 1018s ---- 1018s 25 pairs aligned concordantly 0 times; of these: 1018s 0 (0.00%) aligned discordantly 1 time 1018s ---- 1018s 25 pairs aligned 0 times concordantly or discordantly; of these: 1018s 50 mates make up the pairs; of these: 1018s 50 (100.00%) aligned 0 times 1018s 0 (0.00%) aligned exactly 1 time 1018s 0 (0.00%) aligned >1 times 1018s 0.00% overall alignment rate 1018s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1018s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1018s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1018s Flattened IUPAC characters 1018s Mutating sequence Sim.pm.2 1018s Introducing 4 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1018s Finished SNPs 1018s Finished ref gaps 1018s Finished read gaps 1018s Mutating sequence Sim.pm.1 1018s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1018s Finished SNPs 1018s Finished ref gaps 1018s Finished read gaps 1018s Mutated reference genome to subject genome 1018s SNPs introduced: 7 1018s Reference gaps introduced: 0 1018s Read gaps introduced: 0 1018s Rearrangements introduced: 3 1018s Created read sampler 1018s Sampling 81 reads 1018s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1018s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1018s *** Run 38 of 100 1018s /usr/bin/bowtie2 --large-index --local --rdg 5.53294449266991,3.86472151218975 --mp 7.22794961807119,6.15975625234623 --mm --cp-ival 1 --cp-min 4 --score-min L,9.17821142549998,2.23984202993408 --rfg 41.4194875097165 -i S --trim5 1 -D 28 -f -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta 1018s parsing sequence Sim.pm.1... 1018s parsing sequence Sim.pm.2... 1018s Parsed 81 reference bases 1018s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #2 of read '6' because it was < 2 characters long 1018s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1018s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1018s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #2 of read '31' because it was < 2 characters long 1018s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 1018s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1018s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #2 of read '51' because it was < 2 characters long 1018s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #2 of read '53' because it was < 2 characters long 1018s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #2 of read '55' because it was < 2 characters long 1018s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 1018s Warning: skipping mate #2 of read '56' because it was < 2 characters long 1018s Read 50 alignments... 1018s Read 100 alignments... 1018s 81 reads; of these: 1018s 80 (98.77%) were paired; of these: 1018s 80 (100.00%) aligned concordantly 0 times 1018s 0 (0.00%) aligned concordantly exactly 1 time 1018s 0 (0.00%) aligned concordantly >1 times 1018s ---- 1018s 80 pairs aligned concordantly 0 times; of these: 1018s 0 (0.00%) aligned discordantly 1 time 1018s ---- 1018s 80 pairs aligned 0 times concordantly or discordantly; of these: 1018s 160 mates make up the pairs; of these: 1018s 160 (100.00%) aligned 0 times 1018s 0 (0.00%) aligned exactly 1 time 1018s 0 (0.00%) aligned >1 times 1018s 1 (1.23%) were unpaired; of these: 1018s 1 (100.00%) aligned 0 times 1018s 0 (0.00%) aligned exactly 1 time 1018s 0 (0.00%) aligned >1 times 1018s 0.00% overall alignment rate 1018s Read 150 alignments... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s Processing line... 1018s --- Summary --- 1018s Read 1 reference strings 1018s Checked 0 alignments, 0 edits 1018s --------------- 1018s PASSED 1018s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1018s /usr/bin/bowtie2 --large-index --local --rdg 5.53294449266991,3.86472151218975 --mp 7.22794961807119,6.15975625234623 --mm --cp-ival 1 --cp-min 4 --score-min L,9.17821142549998,2.23984202993408 --rfg 41.4194875097165 -i S --trim5 1 -D 28 -f -p 4 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1019s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #2 of read '6' because it was < 2 characters long 1019s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1019s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 1019s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1019s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1019s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1019s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #2 of read '51' because it was < 2 characters long 1019s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #2 of read '53' because it was < 2 characters long 1019s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #2 of read '55' because it was < 2 characters long 1019s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #2 of read '56' because it was < 2 characters long 1019s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #2 of read '31' because it was < 2 characters long 1019s 81 reads; of these: 1019s 80 (98.77%) were paired; of these: 1019s 80 (100.00%) aligned concordantly 0 times 1019s 0 (0.00%) aligned concordantly exactly 1 time 1019s 0 (0.00%) aligned concordantly >1 times 1019s ---- 1019s 80 pairs aligned concordantly 0 times; of these: 1019s 0 (0.00%) aligned discordantly 1 time 1019s ---- 1019s 80 pairs aligned 0 times concordantly or discordantly; of these: 1019s 160 mates make up the pairs; of these: 1019s 160 (100.00%) aligned 0 times 1019s 0 (0.00%) aligned exactly 1 time 1019s 0 (0.00%) aligned >1 times 1019s 1 (1.23%) were unpaired; of these: 1019s 1 (100.00%) aligned 0 times 1019s 0 (0.00%) aligned exactly 1 time 1019s 0 (0.00%) aligned >1 times 1019s 0.00% overall alignment rate 1019s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1019s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1019s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1019s Flattened IUPAC characters 1019s Mutating sequence Sim.pm.2 1019s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1019s Finished SNPs 1019s Finished ref gaps 1019s Finished read gaps 1019s Mutating sequence Sim.pm.1 1019s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1019s Finished SNPs 1019s Finished ref gaps 1019s Finished read gaps 1019s Mutated reference genome to subject genome 1019s SNPs introduced: 15 1019s Reference gaps introduced: 0 1019s Read gaps introduced: 0 1019s Rearrangements introduced: 1 1019s Created read sampler 1019s Sampling 104 reads 1019s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1019s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1019s parsing sequence Sim.pm.1... 1019s parsing sequence Sim.pm.2... 1019s Parsed 81 reference bases 1019s *** Run 39 of 100 1019s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 2 --large-index --ma 18.249342342929 --mp 5.76285013409437,4.44860420987539 --rdg 2.38901859431834 -R 2 --score-min L,7.25562239285927,7.31182249007044 --rfg 27.9276223638318 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1019s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1019s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #2 of read '50' because it was < 2 characters long 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1019s Read 50 alignments... 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1019s Read 100 alignments... 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1019s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #2 of read '72' because it was < 2 characters long 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1019s 104 reads; of these: 1019s 104 (100.00%) were paired; of these: 1019s 101 (97.12%) aligned concordantly 0 times 1019s 0 (0.00%) aligned concordantly exactly 1 time 1019s 3 (2.88%) aligned concordantly >1 times 1019s ---- 1019s 101 pairs aligned concordantly 0 times; of these: 1019s 0 (0.00%) aligned discordantly 1 time 1019s ---- 1019s 101 pairs aligned 0 times concordantly or discordantly; of these: 1019s 202 mates make up the pairs; of these: 1019s 184 (91.09%) aligned 0 times 1019s 3 (1.49%) aligned exactly 1 time 1019s 15 (7.43%) aligned >1 times 1019s 11.54% overall alignment rate 1019s Read 150 alignments... 1019s Read 200 alignments... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s CCGT 1019s CCGT 1019s Processing line... 1019s TCG 1019s TCG 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s GGG 1019s GGG 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s GT 1019s GT 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s AGACGG 1019s AGACGG 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s GCGTAG 1019s GCGTAG 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s AT 1019s AT 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s CGCGTA 1019s CGCGTA 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s TCCCG 1019s TCCCG 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s GA 1019s GA 1019s Processing line... 1019s AA 1019s AA 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s GAT 1019s GAT 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s GCGTA 1019s GCGTA 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s TCGCGT 1019s TCGCGT 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s ACGGACG 1019s ACGGACG 1019s Processing line... 1019s CCG 1019s CCG 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s ATCGCGTA 1019s ATCGCGTA 1019s Processing line... 1019s Processing line... 1019s TG 1019s TG 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s GTATCGCGTA 1019s GTATCGCGTA 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s CGA 1019s CGA 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s GG 1019s GG 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s ATCCC 1019s ATCCC 1019s Processing line... 1019s Processing line... 1019s AAAG 1019s AAAG 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s TGACA 1019s TGACA 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s Processing line... 1019s --- Summary --- 1019s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 2 --large-index --ma 18.249342342929 --mp 5.76285013409437,4.44860420987539 --rdg 2.38901859431834 -R 2 --score-min L,7.25562239285927,7.31182249007044 --rfg 27.9276223638318 -q -p 4 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1019s Read 1 reference strings 1019s Checked 24 alignments, 0 edits 1019s --------------- 1019s PASSED 1019s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1019s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1019s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #2 of read '72' because it was < 2 characters long 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1019s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 1019s Warning: skipping mate #2 of read '50' because it was < 2 characters long 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1019s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1019s 104 reads; of these: 1019s 104 (100.00%) were paired; of these: 1019s 101 (97.12%) aligned concordantly 0 times 1019s 0 (0.00%) aligned concordantly exactly 1 time 1019s 3 (2.88%) aligned concordantly >1 times 1019s ---- 1019s 101 pairs aligned concordantly 0 times; of these: 1019s 0 (0.00%) aligned discordantly 1 time 1019s ---- 1019s 101 pairs aligned 0 times concordantly or discordantly; of these: 1019s 202 mates make up the pairs; of these: 1019s 184 (91.09%) aligned 0 times 1019s 3 (1.49%) aligned exactly 1 time 1019s 15 (7.43%) aligned >1 times 1019s 11.54% overall alignment rate 1019s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1019s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1019s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1019s Flattened IUPAC characters 1019s Mutating sequence Sim.pm.2 1019s Introducing 3 SNPs, 1/0 ref/read gaps, and 3 rearrangements 1019s Finished SNPs 1019s Finished ref gaps 1019s Finished read gaps 1019s Mutating sequence Sim.pm.1 1019s Introducing 2 SNPs, 0/3 ref/read gaps, and 0 rearrangements 1019s Finished SNPs 1019s Finished ref gaps 1019s Finished read gaps 1019s Mutated reference genome to subject genome 1019s SNPs introduced: 5 1019s Reference gaps introduced: 1 1019s Read gaps introduced: 3 1019s Rearrangements introduced: 3 1019s Created read sampler 1019s Sampling 99 reads 1019s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1019s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1019s *** Run 40 of 100 1019s /usr/bin/bowtie2 -k 2 --large-index --local --cp-ival 2 --cp-min 3 --score-min L,5.73925307664858,5.7959304771638 --gbar 1 --n-ceil 0.630106194205129,0.691612304554808 --trim5 5 --np 5 --nofw -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1019s parsing sequence Sim.pm.1... 1019s parsing sequence Sim.pm.2... 1019s Parsed 81 reference bases 1020s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '7' because it was < 2 characters long 1020s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 1020s Warning: skipping read '16' because it was < 2 characters long 1020s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '23' because it was < 2 characters long 1020s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '25' because it was < 2 characters long 1020s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '30' because it was < 2 characters long 1020s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '34' because it was < 2 characters long 1020s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 1020s Warning: skipping read '35' because it was < 2 characters long 1020s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '37' because it was < 2 characters long 1020s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '47' because it was < 2 characters long 1020s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1020s Warning: skipping read '52' because it was < 2 characters long 1020s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '54' because it was < 2 characters long 1020s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '70' because it was < 2 characters long 1020s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 1020s Warning: skipping read '72' because it was < 2 characters long 1020s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '74' because it was < 2 characters long 1020s 99 reads; of these: 1020s 99 (100.00%) were unpaired; of these: 1020s 99 (100.00%) aligned 0 times 1020s 0 (0.00%) aligned exactly 1 time 1020s 0 (0.00%) aligned >1 times 1020s 0.00% overall alignment rate 1020s Read 50 alignments... 1020s Read 100 alignments... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s --- Summary --- 1020s Read 1 reference strings 1020s Checked 0 alignments, 0 edits 1020s --------------- 1020s PASSED 1020s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1020s /usr/bin/bowtie2 -k 2 --large-index --local --cp-ival 2 --cp-min 3 --score-min L,5.73925307664858,5.7959304771638 --gbar 1 --n-ceil 0.630106194205129,0.691612304554808 --trim5 5 --np 5 --nofw -r -p 4 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1020s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '7' because it was < 2 characters long 1020s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 1020s Warning: skipping read '16' because it was < 2 characters long 1020s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '23' because it was < 2 characters long 1020s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '25' because it was < 2 characters long 1020s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '30' because it was < 2 characters long 1020s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '34' because it was < 2 characters long 1020s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 1020s Warning: skipping read '35' because it was < 2 characters long 1020s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '37' because it was < 2 characters long 1020s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '47' because it was < 2 characters long 1020s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '70' because it was < 2 characters long 1020s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 1020s Warning: skipping read '72' because it was < 2 characters long 1020s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '74' because it was < 2 characters long 1020s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1020s Warning: skipping read '52' because it was < 2 characters long 1020s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '54' because it was < 2 characters long 1020s 99 reads; of these: 1020s 99 (100.00%) were unpaired; of these: 1020s 99 (100.00%) aligned 0 times 1020s 0 (0.00%) aligned exactly 1 time 1020s 0 (0.00%) aligned >1 times 1020s 0.00% overall alignment rate 1020s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1020s Flattened IUPAC characters 1020s Mutating sequence Sim.pm.2 1020s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1020s Finished SNPs 1020s Finished ref gaps 1020s Finished read gaps 1020s Mutating sequence Sim.pm.1 1020s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1020s Finished SNPs 1020s Finished ref gaps 1020s Finished read gaps 1020s Mutated reference genome to subject genome 1020s SNPs introduced: 2 1020s Reference gaps introduced: 2 1020s Read gaps introduced: 0 1020s Rearrangements introduced: 0 1020s Created read sampler 1020s Sampling 204 reads 1020s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1020s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1020s parsing sequence Sim.pm.1... 1020s parsing sequence Sim.pm.2... 1020s Parsed 81 reference bases 1020s *** Run 41 of 100 1020s /usr/bin/bowtie2 --trim3 9 --local --large-index --cp-min 2 --cp-ival 1 --trim5 7 --score-min L,3.86646997679488,8.61663161051166 --nofw --norc -N 0 -L18 -D 8 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1020s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1020s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '5' because it was < 2 characters long 1020s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '7' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1020s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '20' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1020s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '29' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '33' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1020s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '36' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '37' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1020s Warning: skipping mate #2 of read '38' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1020s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '56' because it was < 2 characters long 1020s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '57' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1020s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 1020s Warning: skipping mate #2 of read '71' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '72' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1020s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '75' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '76' because it was < 2 characters long 1020s Read 50 alignments... 1020s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1020s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '92' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '93' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '95' because it was < 2 characters long 1020s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '96' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '99' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '101' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '107' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '108' because it was < 2 characters long 1020s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '110' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '115' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '120' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '127' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '129' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '133' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '134' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '138' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '143' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '145' because it was < 2 characters long 1020s Read 100 alignments... 1020s Read 150 alignments... 1020s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '147' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '150' because it was < 2 characters long 1020s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '152' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '153' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '153' because it was < 2 characters long 1020s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '154' because it was < 2 characters long 1020s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '156' because it was < 2 characters long 1020s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '158' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '159' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '159' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '160' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '160' because it was < 2 characters long 1020s Warning: skipping read '161' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '161' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '163' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '163' because it was < 2 characters long 1020s Warning: skipping read '169' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '169' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '175' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '175' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '178' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '182' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '182' because it was < 2 characters long 1020s Warning: skipping read '184' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '184' because it was < 2 characters long 1020s Warning: skipping mate #1 of read '191' because length (0) <= # seed mismatches (0) 1020s Warning: skipping mate #1 of read '191' because it was < 2 characters long 1020s Warning: skipping read '198' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '198' because it was < 2 characters long 1020s Warning: skipping read '200' because length (0) <= # seed mismatches (0) 1020s Warning: skipping read '200' because it was < 2 characters long 1020s Read 200 alignments... 1020s 204 reads; of these: 1020s 139 (68.14%) were paired; of these: 1020s 139 (100.00%) aligned concordantly 0 times 1020s 0 (0.00%) aligned concordantly exactly 1 time 1020s 0 (0.00%) aligned concordantly >1 times 1020s ---- 1020s 139 pairs aligned concordantly 0 times; of these: 1020s 0 (0.00%) aligned discordantly 1 time 1020s ---- 1020s 139 pairs aligned 0 times concordantly or discordantly; of these: 1020s 278 mates make up the pairs; of these: 1020s 278 (100.00%) aligned 0 times 1020s 0 (0.00%) aligned exactly 1 time 1020s 0 (0.00%) aligned >1 times 1020s 65 (31.86%) were unpaired; of these: 1020s 65 (100.00%) aligned 0 times 1020s 0 (0.00%) aligned exactly 1 time 1020s 0 (0.00%) aligned >1 times 1020s 0.00% overall alignment rate 1020s Read 250 alignments... 1020s Read 300 alignments... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing 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line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s Processing line... 1020s --- Summary --- 1020s Read 1 reference strings 1020s Checked 0 alignments, 0 edits 1020s --------------- 1020s PASSED 1020s ALSO checking that bowtie2 and bowtie2-align match up 1020s /usr/bin/bowtie2 --trim3 9 --local --large-index --cp-min 2 --cp-ival 1 --trim5 7 --score-min L,3.86646997679488,8.61663161051166 --nofw --norc -N 0 -L18 -D 8 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1021s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1021s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '5' because it was < 2 characters long 1021s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '7' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1021s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '20' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1021s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '29' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '33' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1021s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '36' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '37' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1021s Warning: skipping mate #2 of read '38' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1021s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '56' because it was < 2 characters long 1021s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '57' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1021s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #2 of read '71' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '72' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1021s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '75' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '76' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1021s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '92' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '93' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '95' because it was < 2 characters long 1021s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '96' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '99' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '101' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '107' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '108' because it was < 2 characters long 1021s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '110' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '115' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '120' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '127' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '129' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '133' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '134' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '138' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '143' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '145' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '147' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '150' because it was < 2 characters long 1021s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '152' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '153' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '153' because it was < 2 characters long 1021s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '154' because it was < 2 characters long 1021s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '156' because it was < 2 characters long 1021s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '158' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '159' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '159' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '160' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '160' because it was < 2 characters long 1021s Warning: skipping read '161' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '161' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '163' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '163' because it was < 2 characters long 1021s Warning: skipping read '169' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '169' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '175' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '175' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '178' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '182' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '182' because it was < 2 characters long 1021s Warning: skipping read '184' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '184' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '191' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '191' because it was < 2 characters long 1021s Warning: skipping read '198' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '198' because it was < 2 characters long 1021s Warning: skipping read '200' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '200' because it was < 2 characters long 1021s 204 reads; of these: 1021s 139 (68.14%) were paired; of these: 1021s 139 (100.00%) aligned concordantly 0 times 1021s 0 (0.00%) aligned concordantly exactly 1 time 1021s 0 (0.00%) aligned concordantly >1 times 1021s ---- 1021s 139 pairs aligned concordantly 0 times; of these: 1021s 0 (0.00%) aligned discordantly 1 time 1021s ---- 1021s 139 pairs aligned 0 times concordantly or discordantly; of these: 1021s 278 mates make up the pairs; of these: 1021s 278 (100.00%) aligned 0 times 1021s 0 (0.00%) aligned exactly 1 time 1021s 0 (0.00%) aligned >1 times 1021s 65 (31.86%) were unpaired; of these: 1021s 65 (100.00%) aligned 0 times 1021s 0 (0.00%) aligned exactly 1 time 1021s 0 (0.00%) aligned >1 times 1021s 0.00% overall alignment rate 1021s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1021s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1021s /usr/bin/bowtie2 --trim3 9 --local --large-index --cp-min 2 --cp-ival 1 --trim5 7 --score-min L,3.86646997679488,8.61663161051166 --nofw --norc -N 0 -L18 -D 8 -q -p 4 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1021s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1021s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '5' because it was < 2 characters long 1021s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '7' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1021s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '20' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1021s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '29' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '33' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1021s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '36' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '37' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1021s Warning: skipping mate #2 of read '38' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1021s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #2 of read '71' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '72' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1021s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '75' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '76' because it was < 2 characters long 1021s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '56' because it was < 2 characters long 1021s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '57' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '129' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1021s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '92' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '93' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '95' because it was < 2 characters long 1021s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '96' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '145' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '115' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '99' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '101' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '107' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '108' because it was < 2 characters long 1021s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '110' because it was < 2 characters long 1021s Warning: skipping read '161' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '161' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '133' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '134' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '138' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '143' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '120' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '127' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '147' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '150' because it was < 2 characters long 1021s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '152' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '153' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '153' because it was < 2 characters long 1021s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '154' because it was < 2 characters long 1021s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '156' because it was < 2 characters long 1021s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '158' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '159' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '159' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '160' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '160' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '163' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '163' because it was < 2 characters long 1021s Warning: skipping read '169' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '169' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '175' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '175' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '178' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '182' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '182' because it was < 2 characters long 1021s Warning: skipping read '184' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '184' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '191' because length (0) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '191' because it was < 2 characters long 1021s Warning: skipping read '198' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '198' because it was < 2 characters long 1021s Warning: skipping read '200' because length (0) <= # seed mismatches (0) 1021s Warning: skipping read '200' because it was < 2 characters long 1021s 204 reads; of these: 1021s 139 (68.14%) were paired; of these: 1021s 139 (100.00%) aligned concordantly 0 times 1021s 0 (0.00%) aligned concordantly exactly 1 time 1021s 0 (0.00%) aligned concordantly >1 times 1021s ---- 1021s 139 pairs aligned concordantly 0 times; of these: 1021s 0 (0.00%) aligned discordantly 1 time 1021s ---- 1021s 139 pairs aligned 0 times concordantly or discordantly; of these: 1021s 278 mates make up the pairs; of these: 1021s 278 (100.00%) aligned 0 times 1021s 0 (0.00%) aligned exactly 1 time 1021s 0 (0.00%) aligned >1 times 1021s 65 (31.86%) were unpaired; of these: 1021s 65 (100.00%) aligned 0 times 1021s 0 (0.00%) aligned exactly 1 time 1021s 0 (0.00%) aligned >1 times 1021s 0.00% overall alignment rate 1021s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1021s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1021s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1021s Flattened IUPAC characters 1021s Mutating sequence Sim.pm.2 1021s Introducing 4 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1021s Finished SNPs 1021s Finished ref gaps 1021s Finished read gaps 1021s Mutating sequence Sim.pm.1 1021s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1021s Finished SNPs 1021s Finished ref gaps 1021s Finished read gaps 1021s Mutated reference genome to subject genome 1021s SNPs introduced: 10 1021s Reference gaps introduced: 1 1021s Read gaps introduced: 1 1021s Rearrangements introduced: 0 1021s Created read sampler 1021s Sampling 98 reads 1021s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1021s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1021s parsing sequence Sim.pm.1... 1021s parsing sequence Sim.pm.2... 1021s Parsed 81 reference bases 1021s *** Run 42 of 100 1021s /usr/bin/bowtie2 --score-min L,5.34275038360329,5.99730359240007 -R 2 --large-index -M 3 --local --mm --cp-ival 1 --cp-min 6 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1021s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1021s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #2 of read '3' because it was < 2 characters long 1021s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '37' because it was < 2 characters long 1021s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #2 of read '44' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1021s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1021s Read 50 alignments... 1021s Read 100 alignments... 1021s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (0) 1021s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1021s 98 reads; of these: 1021s 98 (100.00%) were paired; of these: 1021s 98 (100.00%) aligned concordantly 0 times 1021s 0 (0.00%) aligned concordantly exactly 1 time 1021s 0 (0.00%) aligned concordantly >1 times 1021s ---- 1021s 98 pairs aligned concordantly 0 times; of these: 1021s 0 (0.00%) aligned discordantly 1 time 1021s ---- 1021s 98 pairs aligned 0 times concordantly or discordantly; of these: 1021s 196 mates make up the pairs; of these: 1021s 196 (100.00%) aligned 0 times 1021s 0 (0.00%) aligned exactly 1 time 1021s 0 (0.00%) aligned >1 times 1021s 0.00% overall alignment rate 1021s Read 150 alignments... 1021s Read 200 alignments... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 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1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s Processing line... 1021s --- Summary --- 1021s Read 1 reference strings 1021s Checked 0 alignments, 0 edits 1021s --------------- 1021s PASSED 1021s Flattened IUPAC characters 1021s Mutating sequence Sim.pm.1 1021s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1021s Finished SNPs 1021s Finished ref gaps 1021s Finished read gaps 1021s Mutating sequence Sim.pm.2 1021s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1021s Finished SNPs 1021s Finished ref gaps 1021s Finished read gaps 1021s Mutated reference genome to subject genome 1021s SNPs introduced: 3 1021s Reference gaps introduced: 1 1021s Read gaps introduced: 0 1021s Rearrangements introduced: 0 1021s Created read sampler 1021s Sampling 49 reads 1021s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1021s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1021s parsing sequence Sim.pm.1... 1021s parsing sequence Sim.pm.2... 1021s Parsed 81 reference bases 1021s *** Run 43 of 100 1021s /usr/bin/bowtie2 -N 0 -L17 --rfg 12.7056525461285 --trim5 3 --score-min L,5.1754641732734,6.64177577688868 --cp-min 7 --cp-ival 3 --local --trim3 9 --mp 5.74441370147987,2.43650553380278 --large-index --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1022s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1022s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 1022s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1022s 49 reads; of these: 1022s 49 (100.00%) were unpaired; of these: 1022s 49 (100.00%) aligned 0 times 1022s 0 (0.00%) aligned exactly 1 time 1022s 0 (0.00%) aligned >1 times 1022s 0.00% overall alignment rate 1022s Read 50 alignments... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s --- Summary --- 1022s Read 1 reference strings 1022s Checked 0 alignments, 0 edits 1022s --------------- 1022s PASSED 1022s Flattened IUPAC characters 1022s Mutating sequence Sim.pm.1 1022s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1022s Finished SNPs 1022s Finished ref gaps 1022s Finished read gaps 1022s Mutating sequence Sim.pm.2 1022s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1022s Finished SNPs 1022s Finished ref gaps 1022s Finished read gaps 1022s Mutated reference genome to subject genome 1022s SNPs introduced: 4 1022s Reference gaps introduced: 0 1022s Read gaps introduced: 0 1022s Rearrangements introduced: 1 1022s Created read sampler 1022s Sampling 84 reads 1022s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1022s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1022s parsing sequence Sim.pm.1... 1022s parsing sequence Sim.pm.2... 1022s Parsed 81 reference bases 1022s *** Run 44 of 100 1022s /usr/bin/bowtie2 --nofw --score-min L,7.37634835717716,5.10034967378235 --gbar 4 --trim5 2 --rfg 36.4856556953307 --cp-ival 1 --mm --cp-min 3 --large-index -k 2 --rdg 47.3637743461508,13.5619183149017 --local -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1022s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1022s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1022s Read 50 alignments... 1022s Read 100 alignments... 1022s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1022s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '81' because it was < 2 characters long 1022s 84 reads; of these: 1022s 80 (95.24%) were paired; of these: 1022s 80 (100.00%) aligned concordantly 0 times 1022s 0 (0.00%) aligned concordantly exactly 1 time 1022s 0 (0.00%) aligned concordantly >1 times 1022s ---- 1022s 80 pairs aligned concordantly 0 times; of these: 1022s 0 (0.00%) aligned discordantly 1 time 1022s ---- 1022s 80 pairs aligned 0 times concordantly or discordantly; of these: 1022s 160 mates make up the pairs; of these: 1022s 160 (100.00%) aligned 0 times 1022s 0 (0.00%) aligned exactly 1 time 1022s 0 (0.00%) aligned >1 times 1022s 4 (4.76%) were unpaired; of these: 1022s 4 (100.00%) aligned 0 times 1022s 0 (0.00%) aligned exactly 1 time 1022s 0 (0.00%) aligned >1 times 1022s 0.00% overall alignment rate 1022s Read 150 alignments... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s 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Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s Processing line... 1022s --- Summary --- 1022s Read 1 reference strings 1022s Checked 0 alignments, 0 edits 1022s --------------- 1022s PASSED 1022s ALSO checking that bowtie2 and bowtie2-align match up 1022s /usr/bin/bowtie2 --nofw --score-min L,7.37634835717716,5.10034967378235 --gbar 4 --trim5 2 --rfg 36.4856556953307 --cp-ival 1 --mm --cp-min 3 --large-index -k 2 --rdg 47.3637743461508,13.5619183149017 --local -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1022s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1022s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1022s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1022s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '81' because it was < 2 characters long 1022s 84 reads; of these: 1022s 80 (95.24%) were paired; of these: 1022s 80 (100.00%) aligned concordantly 0 times 1022s 0 (0.00%) aligned concordantly exactly 1 time 1022s 0 (0.00%) aligned concordantly >1 times 1022s ---- 1022s 80 pairs aligned concordantly 0 times; of these: 1022s 0 (0.00%) aligned discordantly 1 time 1022s ---- 1022s 80 pairs aligned 0 times concordantly or discordantly; of these: 1022s 160 mates make up the pairs; of these: 1022s 160 (100.00%) aligned 0 times 1022s 0 (0.00%) aligned exactly 1 time 1022s 0 (0.00%) aligned >1 times 1022s 4 (4.76%) were unpaired; of these: 1022s 4 (100.00%) aligned 0 times 1022s 0 (0.00%) aligned exactly 1 time 1022s 0 (0.00%) aligned >1 times 1022s 0.00% overall alignment rate 1022s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1022s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1022s /usr/bin/bowtie2 --nofw --score-min L,7.37634835717716,5.10034967378235 --gbar 4 --trim5 2 --rfg 36.4856556953307 --cp-ival 1 --mm --cp-min 3 --large-index -k 2 --rdg 47.3637743461508,13.5619183149017 --local -r -p 4 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1022s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1022s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1022s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1022s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 1022s Warning: skipping mate #1 of read '81' because it was < 2 characters long 1022s 84 reads; of these: 1022s 80 (95.24%) were paired; of these: 1022s 80 (100.00%) aligned concordantly 0 times 1022s 0 (0.00%) aligned concordantly exactly 1 time 1022s 0 (0.00%) aligned concordantly >1 times 1022s ---- 1022s 80 pairs aligned concordantly 0 times; of these: 1022s 0 (0.00%) aligned discordantly 1 time 1022s ---- 1022s 80 pairs aligned 0 times concordantly or discordantly; of these: 1022s 160 mates make up the pairs; of these: 1022s 160 (100.00%) aligned 0 times 1022s 0 (0.00%) aligned exactly 1 time 1022s 0 (0.00%) aligned >1 times 1022s 4 (4.76%) were unpaired; of these: 1022s 4 (100.00%) aligned 0 times 1022s 0 (0.00%) aligned exactly 1 time 1022s 0 (0.00%) aligned >1 times 1022s 0.00% overall alignment rate 1022s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1022s Flattened IUPAC characters 1022s Mutating sequence Sim.pm.2 1022s Introducing 9 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1022s Finished SNPs 1022s Finished ref gaps 1022s Finished read gaps 1022s Mutating sequence Sim.pm.1 1022s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1022s Finished SNPs 1022s Finished ref gaps 1022s Finished read gaps 1022s Mutated reference genome to subject genome 1022s SNPs introduced: 9 1022s Reference gaps introduced: 1 1022s Read gaps introduced: 0 1022s Rearrangements introduced: 2 1022s Created read sampler 1022s Sampling 32 reads 1022s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1022s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1022s parsing sequence Sim.pm.1... 1022s parsing sequence Sim.pm.2... 1022s Parsed 81 reference bases 1022s *** Run 45 of 100 1022s /usr/bin/bowtie2 --large-index --rdg 33.0454858964618 -a --mp 8.04119972768332,1.02496926725022 --local --mm --cp-ival 4 --cp-min 3 --n-ceil 1.49677123838363,0.843823349208098 --gbar 5 --score-min L,6.77738606979969,6.15365158629622 --trim5 5 --rfg 46.0932506834745,12.4964397587801 --np 3 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1023s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1023s Warning: skipping read '2' because it was < 2 characters long 1023s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '3' because it was < 2 characters long 1023s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1023s Warning: skipping read '4' because it was < 2 characters long 1023s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '18' because it was < 2 characters long 1023s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '26' because it was < 2 characters long 1023s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '27' because it was < 2 characters long 1023s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '30' because it was < 2 characters long 1023s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '31' because it was < 2 characters long 1023s 32 reads; of these: 1023s 32 (100.00%) were unpaired; of these: 1023s 32 (100.00%) aligned 0 times 1023s 0 (0.00%) aligned exactly 1 time 1023s 0 (0.00%) aligned >1 times 1023s 0.00% overall alignment rate 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s --- Summary --- 1023s /usr/bin/bowtie2 --large-index --rdg 33.0454858964618 -a --mp 8.04119972768332,1.02496926725022 --local --mm --cp-ival 4 --cp-min 3 --n-ceil 1.49677123838363,0.843823349208098 --gbar 5 --score-min L,6.77738606979969,6.15365158629622 --trim5 5 --rfg 46.0932506834745,12.4964397587801 --np 3 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1023s Read 1 reference strings 1023s Checked 0 alignments, 0 edits 1023s --------------- 1023s PASSED 1023s ALSO checking that bowtie2 and bowtie2-align match up 1023s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1023s Warning: skipping read '2' because it was < 2 characters long 1023s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '3' because it was < 2 characters long 1023s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1023s Warning: skipping read '4' because it was < 2 characters long 1023s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '18' because it was < 2 characters long 1023s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '26' because it was < 2 characters long 1023s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '27' because it was < 2 characters long 1023s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '30' because it was < 2 characters long 1023s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '31' because it was < 2 characters long 1023s 32 reads; of these: 1023s 32 (100.00%) were unpaired; of these: 1023s 32 (100.00%) aligned 0 times 1023s 0 (0.00%) aligned exactly 1 time 1023s 0 (0.00%) aligned >1 times 1023s 0.00% overall alignment rate 1023s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1023s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1023s /usr/bin/bowtie2 --large-index --rdg 33.0454858964618 -a --mp 8.04119972768332,1.02496926725022 --local --mm --cp-ival 4 --cp-min 3 --n-ceil 1.49677123838363,0.843823349208098 --gbar 5 --score-min L,6.77738606979969,6.15365158629622 --trim5 5 --rfg 46.0932506834745,12.4964397587801 --np 3 -r -p 2 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1023s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1023s Warning: skipping read '2' because it was < 2 characters long 1023s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '3' because it was < 2 characters long 1023s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1023s Warning: skipping read '4' because it was < 2 characters long 1023s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '18' because it was < 2 characters long 1023s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '26' because it was < 2 characters long 1023s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '27' because it was < 2 characters long 1023s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '30' because it was < 2 characters long 1023s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '31' because it was < 2 characters long 1023s 32 reads; of these: 1023s 32 (100.00%) were unpaired; of these: 1023s 32 (100.00%) aligned 0 times 1023s 0 (0.00%) aligned exactly 1 time 1023s 0 (0.00%) aligned >1 times 1023s 0.00% overall alignment rate 1023s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1023s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1023s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1023s Flattened IUPAC characters 1023s Mutating sequence Sim.pm.2 1023s Introducing 2 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1023s Finished SNPs 1023s Finished ref gaps 1023s Finished read gaps 1023s Mutating sequence Sim.pm.1 1023s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1023s Finished SNPs 1023s Finished ref gaps 1023s Finished read gaps 1023s Mutated reference genome to subject genome 1023s SNPs introduced: 8 1023s Reference gaps introduced: 1 1023s Read gaps introduced: 2 1023s Rearrangements introduced: 1 1023s Created read sampler 1023s Sampling 82 reads 1023s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1023s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1023s parsing sequence Sim.pm.1... 1023s parsing sequence Sim.pm.2... 1023s Parsed 81 reference bases 1023s *** Run 46 of 100 1023s /usr/bin/bowtie2 --trim5 9 --rfg 48.4940039911263 --gbar 3 --score-min L,6.13476180166693,1.18815191136343 --np 1 --nofw -N 0 -L14 -R 1 -D 38 --local --large-index --cp-min 2 --mm --cp-ival 1 -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta 1023s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '3' because it was < 2 characters long 1023s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '8' because it was < 2 characters long 1023s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '10' because it was < 2 characters long 1023s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '17' because it was < 2 characters long 1023s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '19' because it was < 2 characters long 1023s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '20' because it was < 2 characters long 1023s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '27' because it was < 2 characters long 1023s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '32' because it was < 2 characters long 1023s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '43' because it was < 2 characters long 1023s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '44' because it was < 2 characters long 1023s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '47' because it was < 2 characters long 1023s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '48' because it was < 2 characters long 1023s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '51' because it was < 2 characters long 1023s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '65' because it was < 2 characters long 1023s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '67' because it was < 2 characters long 1023s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '68' because it was < 2 characters long 1023s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 1023s Warning: skipping read '70' because it was < 2 characters long 1023s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '72' because it was < 2 characters long 1023s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '74' because it was < 2 characters long 1023s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '75' because it was < 2 characters long 1023s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '79' because it was < 2 characters long 1023s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1023s Warning: skipping read '80' because it was < 2 characters long 1023s 82 reads; of these: 1023s 82 (100.00%) were unpaired; of these: 1023s 80 (97.56%) aligned 0 times 1023s 1 (1.22%) aligned exactly 1 time 1023s 1 (1.22%) aligned >1 times 1023s 2.44% overall alignment rate 1023s Read 50 alignments... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s /usr/bin/bowtie2 --trim5 9 --rfg 48.4940039911263 --gbar 3 --score-min L,6.13476180166693,1.18815191136343 --np 1 --nofw -N 0 -L14 -R 1 -D 38 --local --large-index --cp-min 2 --mm --cp-ival 1 -f -p 4 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s TATCGCG 1023s TATCGCG 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s ACCGAAAGACGGACGTAGATCCCGTATCGCGTA 1023s ACCGAAAGACGGACGTANATCCCGTATCGCGTA 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s Processing line... 1023s --- Summary --- 1023s Read 1 reference strings 1023s Checked 2 alignments, 0 edits 1023s --------------- 1023s PASSED 1023s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1024s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '3' because it was < 2 characters long 1024s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '8' because it was < 2 characters long 1024s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '10' because it was < 2 characters long 1024s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '43' because it was < 2 characters long 1024s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '44' because it was < 2 characters long 1024s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '47' because it was < 2 characters long 1024s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '48' because it was < 2 characters long 1024s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '17' because it was < 2 characters long 1024s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '19' because it was < 2 characters long 1024s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '20' because it was < 2 characters long 1024s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '27' because it was < 2 characters long 1024s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '32' because it was < 2 characters long 1024s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '65' because it was < 2 characters long 1024s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '67' because it was < 2 characters long 1024s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '51' because it was < 2 characters long 1024s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '68' because it was < 2 characters long 1024s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 1024s Warning: skipping read '70' because it was < 2 characters long 1024s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '72' because it was < 2 characters long 1024s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '74' because it was < 2 characters long 1024s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '75' because it was < 2 characters long 1024s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '79' because it was < 2 characters long 1024s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '80' because it was < 2 characters long 1024s 82 reads; of these: 1024s 82 (100.00%) were unpaired; of these: 1024s 80 (97.56%) aligned 0 times 1024s 1 (1.22%) aligned exactly 1 time 1024s 1 (1.22%) aligned >1 times 1024s 2.44% overall alignment rate 1024s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1024s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1024s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1024s /usr/bin/bowtie2 --trim5 9 --rfg 48.4940039911263 --gbar 3 --score-min L,6.13476180166693,1.18815191136343 --np 1 --nofw -N 0 -L14 -R 1 -D 38 --local --large-index --cp-min 2 --mm --cp-ival 1 -f -p 4 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1024s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1024s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '3' because it was < 2 characters long 1024s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '8' because it was < 2 characters long 1024s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '10' because it was < 2 characters long 1024s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '17' because it was < 2 characters long 1024s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1024s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1024s Warning: skipping read '19' because it was < 2 characters long 1024s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '20' because it was < 2 characters long 1024s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '27' because it was < 2 characters long 1024s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '32' because it was < 2 characters long 1024s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '51' because it was < 2 characters long 1024s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '65' because it was < 2 characters long 1024s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '67' because it was < 2 characters long 1024s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '68' because it was < 2 characters long 1024s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 1024s Warning: skipping read '70' because it was < 2 characters long 1024s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '72' because it was < 2 characters long 1024s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '74' because it was < 2 characters long 1024s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '75' because it was < 2 characters long 1024s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '43' because it was < 2 characters long 1024s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '44' because it was < 2 characters long 1024s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '47' because it was < 2 characters long 1024s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '48' because it was < 2 characters long 1024s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '79' because it was < 2 characters long 1024s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read '80' because it was < 2 characters long 1024s 82 reads; of these: 1024s 82 (100.00%) were unpaired; of these: 1024s 80 (97.56%) aligned 0 times 1024s 1 (1.22%) aligned exactly 1 time 1024s 1 (1.22%) aligned >1 times 1024s 2.44% overall alignment rate 1024s Flattened IUPAC characters 1024s Mutating sequence Sim.pm.2 1024s Introducing 5 SNPs, 0/3 ref/read gaps, and 0 rearrangements 1024s Finished SNPs 1024s Finished ref gaps 1024s Finished read gaps 1024s Mutating sequence Sim.pm.1 1024s Introducing 2 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1024s Finished SNPs 1024s Finished ref gaps 1024s Finished read gaps 1024s Mutated reference genome to subject genome 1024s SNPs introduced: 7 1024s Reference gaps introduced: 0 1024s Read gaps introduced: 5 1024s Rearrangements introduced: 0 1024s Created read sampler 1024s Sampling 92 reads 1024s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1024s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1024s parsing sequence Sim.pm.1... 1024s parsing sequence Sim.pm.2... 1024s Parsed 81 reference bases 1024s *** Run 47 of 100 1024s /usr/bin/bowtie2 --trim5 3 --score-min L,2.29413291812004,9.89890606720327 --gbar 2 --np 1 --mp 4.58981127996648,1.24925474738081 --rdg 23.3638234017068,17.3653157921749 --local --large-index -k 5 --cp-min 3 --cp-ival 3 --mm --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1024s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1024s 92 reads; of these: 1024s 92 (100.00%) were unpaired; of these: 1024s 92 (100.00%) aligned 0 times 1024s 0 (0.00%) aligned exactly 1 time 1024s 0 (0.00%) aligned >1 times 1024s 0.00% overall alignment rate 1024s Read 50 alignments... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s Processing line... 1024s --- Summary --- 1024s Read 1 reference strings 1024s Checked 0 alignments, 0 edits 1024s --------------- 1024s PASSED 1024s ALSO checking that bowtie2 and bowtie2-align match up 1024s /usr/bin/bowtie2 --trim5 3 --score-min L,2.29413291812004,9.89890606720327 --gbar 2 --np 1 --mp 4.58981127996648,1.24925474738081 --rdg 23.3638234017068,17.3653157921749 --local --large-index -k 5 --cp-min 3 --cp-ival 3 --mm --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1024s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1024s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 1024s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1024s 92 reads; of these: 1024s 92 (100.00%) were unpaired; of these: 1024s 92 (100.00%) aligned 0 times 1024s 0 (0.00%) aligned exactly 1 time 1024s 0 (0.00%) aligned >1 times 1024s 0.00% overall alignment rate 1024s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1024s Flattened IUPAC characters 1024s Mutating sequence Sim.pm.2 1024s Introducing 2 SNPs, 2/1 ref/read gaps, and 0 rearrangements 1024s Finished SNPs 1024s Finished ref gaps 1024s Finished read gaps 1024s Mutating sequence Sim.pm.1 1024s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1024s Finished SNPs 1024s Finished ref gaps 1024s Finished read gaps 1024s Mutated reference genome to subject genome 1024s SNPs introduced: 8 1024s Reference gaps introduced: 2 1024s Read gaps introduced: 1 1024s Rearrangements introduced: 1 1024s Created read sampler 1024s Sampling 57 reads 1024s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1024s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1024s parsing sequence Sim.pm.1... 1024s parsing sequence Sim.pm.2... 1024s Parsed 81 reference bases 1024s *** Run 48 of 100 1024s /usr/bin/bowtie2 --large-index --local --trim3 3 --rdg 13.2567233819615 --cp-ival 1 --mm --cp-min 4 --score-min L,7.71073076427547,4.21388660007173 --rfg 35.2845709375984,7.22561163649754 -D 37 -N 0 -L31 --nofw --norc -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1025s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1025s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1025s Warning: skipping mate #2 of read '26' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1025s 57 reads; of these: 1025s 56 (98.25%) were paired; of these: 1025s 56 (100.00%) aligned concordantly 0 times 1025s 0 (0.00%) aligned concordantly exactly 1 time 1025s 0 (0.00%) aligned concordantly >1 times 1025s ---- 1025s 56 pairs aligned concordantly 0 times; of these: 1025s 0 (0.00%) aligned discordantly 1 time 1025s ---- 1025s 56 pairs aligned 0 times concordantly or discordantly; of these: 1025s 112 mates make up the pairs; of these: 1025s 112 (100.00%) aligned 0 times 1025s 0 (0.00%) aligned exactly 1 time 1025s 0 (0.00%) aligned >1 times 1025s 1 (1.75%) were unpaired; of these: 1025s 1 (100.00%) aligned 0 times 1025s 0 (0.00%) aligned exactly 1 time 1025s 0 (0.00%) aligned >1 times 1025s 0.00% overall alignment rate 1025s Read 50 alignments... 1025s Read 100 alignments... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s --- Summary --- 1025s Read 1 reference strings 1025s Checked 0 alignments, 0 edits 1025s --------------- 1025s PASSED 1025s ALSO checking that bowtie2 and bowtie2-align match up 1025s /usr/bin/bowtie2 --large-index --local --trim3 3 --rdg 13.2567233819615 --cp-ival 1 --mm --cp-min 4 --score-min L,7.71073076427547,4.21388660007173 --rfg 35.2845709375984,7.22561163649754 -D 37 -N 0 -L31 --nofw --norc -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1025s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1025s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1025s Warning: skipping mate #2 of read '26' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1025s 57 reads; of these: 1025s 56 (98.25%) were paired; of these: 1025s 56 (100.00%) aligned concordantly 0 times 1025s 0 (0.00%) aligned concordantly exactly 1 time 1025s 0 (0.00%) aligned concordantly >1 times 1025s ---- 1025s 56 pairs aligned concordantly 0 times; of these: 1025s 0 (0.00%) aligned discordantly 1 time 1025s ---- 1025s 56 pairs aligned 0 times concordantly or discordantly; of these: 1025s 112 mates make up the pairs; of these: 1025s 112 (100.00%) aligned 0 times 1025s 0 (0.00%) aligned exactly 1 time 1025s 0 (0.00%) aligned >1 times 1025s 1 (1.75%) were unpaired; of these: 1025s 1 (100.00%) aligned 0 times 1025s 0 (0.00%) aligned exactly 1 time 1025s 0 (0.00%) aligned >1 times 1025s 0.00% overall alignment rate 1025s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1025s Flattened IUPAC characters 1025s Mutating sequence Sim.pm.1 1025s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1025s Finished SNPs 1025s Finished ref gaps 1025s Finished read gaps 1025s Mutating sequence Sim.pm.2 1025s Introducing 3 SNPs, 2/1 ref/read gaps, and 3 rearrangements 1025s Finished SNPs 1025s Finished ref gaps 1025s Finished read gaps 1025s Mutated reference genome to subject genome 1025s SNPs introduced: 10 1025s Reference gaps introduced: 2 1025s Read gaps introduced: 1 1025s Rearrangements introduced: 3 1025s Created read sampler 1025s Sampling 82 reads 1025s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1025s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1025s parsing sequence Sim.pm.1... 1025s parsing sequence Sim.pm.2... 1025s Parsed 81 reference bases 1025s *** Run 49 of 100 1025s /usr/bin/bowtie2 --mm --cp-ival 2 --cp-min 2 --large-index --local --trim3 7 -D 25 --norc --np 2 --score-min L,3.46100285471661,1.30269014077664 --rfg 40.9367145032719,10.500279419368 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1025s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '7' because it was < 2 characters long 1025s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '11' because it was < 2 characters long 1025s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '15' because it was < 2 characters long 1025s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '24' because it was < 2 characters long 1025s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '30' because it was < 2 characters long 1025s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '31' because it was < 2 characters long 1025s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '45' because it was < 2 characters long 1025s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '49' because it was < 2 characters long 1025s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '50' because it was < 2 characters long 1025s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '53' because it was < 2 characters long 1025s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '63' because it was < 2 characters long 1025s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '65' because it was < 2 characters long 1025s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '68' because it was < 2 characters long 1025s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '70' because it was < 2 characters long 1025s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '71' because it was < 2 characters long 1025s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '72' because it was < 2 characters long 1025s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '73' because it was < 2 characters long 1025s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '74' because it was < 2 characters long 1025s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '76' because it was < 2 characters long 1025s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '77' because it was < 2 characters long 1025s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 1025s Warning: skipping read '82' because it was < 2 characters long 1025s 82 reads; of these: 1025s 82 (100.00%) were unpaired; of these: 1025s 77 (93.90%) aligned 0 times 1025s 3 (3.66%) aligned exactly 1 time 1025s 2 (2.44%) aligned >1 times 1025s 6.10% overall alignment rate 1025s Read 50 alignments... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s AGACG 1025s AGACG 1025s Processing line... 1025s GTATC 1025s GTATC 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s TATCGCGTAGAGATGACAACCGAAAGAC 1025s TATCGCGTAGNGATGACAACCGAAAGAC 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s TATCGCGTAGAGATGACAACCGAAAGAC 1025s TATCGCGTAGNGATGACAACCGAAAGAC 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s TCCCGTAT 1025s TCCCGTAT 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s --- Summary --- 1025s Read 1 reference strings 1025s Checked 5 alignments, 0 edits 1025s --------------- 1025s PASSED 1025s Flattened IUPAC characters 1025s Mutating sequence Sim.pm.2 1025s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1025s Finished SNPs 1025s Finished ref gaps 1025s Finished read gaps 1025s Mutating sequence Sim.pm.1 1025s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1025s Finished SNPs 1025s Finished ref gaps 1025s Finished read gaps 1025s Mutated reference genome to subject genome 1025s SNPs introduced: 3 1025s Reference gaps introduced: 2 1025s Read gaps introduced: 1 1025s Rearrangements introduced: 0 1025s Created read sampler 1025s Sampling 69 reads 1025s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1025s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1025s parsing sequence Sim.pm.1... 1025s parsing sequence Sim.pm.2... 1025s Parsed 81 reference bases 1025s *** Run 50 of 100 1025s /usr/bin/bowtie2 --cp-ival 2 --cp-min 7 --np 1 --large-index -k 3 --score-min L,2.75584053818437,3.86326904100267 --rdg 46.5919640880623 --trim5 1 --local -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1025s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (0) 1025s Warning: skipping mate #2 of read '1' because it was < 2 characters long 1025s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 1025s Warning: skipping mate #2 of read '18' because it was < 2 characters long 1025s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 1025s Warning: skipping mate #2 of read '25' because it was < 2 characters long 1025s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 1025s Warning: skipping mate #2 of read '56' because it was < 2 characters long 1025s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1025s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1025s Read 50 alignments... 1025s Read 100 alignments... 1025s 69 reads; of these: 1025s 68 (98.55%) were paired; of these: 1025s 68 (100.00%) aligned concordantly 0 times 1025s 0 (0.00%) aligned concordantly exactly 1 time 1025s 0 (0.00%) aligned concordantly >1 times 1025s ---- 1025s 68 pairs aligned concordantly 0 times; of these: 1025s 0 (0.00%) aligned discordantly 1 time 1025s ---- 1025s 68 pairs aligned 0 times concordantly or discordantly; of these: 1025s 136 mates make up the pairs; of these: 1025s 136 (100.00%) aligned 0 times 1025s 0 (0.00%) aligned exactly 1 time 1025s 0 (0.00%) aligned >1 times 1025s 1 (1.45%) were unpaired; of these: 1025s 1 (100.00%) aligned 0 times 1025s 0 (0.00%) aligned exactly 1 time 1025s 0 (0.00%) aligned >1 times 1025s 0.00% overall alignment rate 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s Processing line... 1025s --- Summary --- 1025s Read 1 reference strings 1025s Checked 0 alignments, 0 edits 1025s --------------- 1025s PASSED 1025s Flattened IUPAC characters 1025s Mutating sequence Sim.pm.1 1025s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1025s Finished SNPs 1025s Finished ref gaps 1025s Finished read gaps 1025s Mutating sequence Sim.pm.2 1025s Introducing 9 SNPs, 0/3 ref/read gaps, and 0 rearrangements 1025s Finished SNPs 1025s Finished ref gaps 1025s Finished read gaps 1025s Mutated reference genome to subject genome 1025s SNPs introduced: 14 1025s Reference gaps introduced: 0 1025s Read gaps introduced: 3 1025s Rearrangements introduced: 0 1025s Created read sampler 1025s Sampling 58 reads 1025s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1025s *** Run 51 of 100 1025s /usr/bin/bowtie2 --np 2 -D 26 -R 2 --rfg 6.63676579907774 --trim5 9 --score-min L,3.26575879267859,1.02716931575415 --cp-min 3 --mm --cp-ival 3 --rdg 20.1692331691202 --mp 5.07947885978767,2.84402674191737 -a --large-index --ma 34.1091081180024 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1025s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1025s parsing sequence Sim.pm.1... 1025s parsing sequence Sim.pm.2... 1025s Parsed 81 reference bases 1026s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1026s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '2' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1026s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '6' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1026s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '7' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1026s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 1026s Warning: skipping read '11' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1026s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '18' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1026s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '19' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1026s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '22' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1026s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '23' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1026s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '27' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1026s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '30' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1026s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '31' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1026s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '34' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1026s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '35' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1026s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '38' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1026s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '39' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1026s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '42' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1026s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '47' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1026s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 1026s Warning: skipping read '49' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1026s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '52' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1026s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '56' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1026s 58 reads; of these: 1026s 58 (100.00%) were unpaired; of these: 1026s 52 (89.66%) aligned 0 times 1026s 3 (5.17%) aligned exactly 1 time 1026s 3 (5.17%) aligned >1 times 1026s 10.34% overall alignment rate 1026s Read 50 alignments... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s ATCGC 1026s ATCGC 1026s Processing line... 1026s ATCGC 1026s ATCGC 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s GT 1026s GT 1026s Processing line... 1026s AC 1026s AC 1026s Processing line... 1026s GT 1026s GT 1026s Processing line... 1026s GT 1026s GT 1026s Processing line... 1026s GT 1026s GT 1026s Processing line... 1026s GT 1026s GT 1026s Processing line... 1026s AC 1026s AC 1026s Processing line... 1026s AC 1026s AC 1026s Processing line... 1026s GT 1026s GT 1026s Processing line... 1026s AC 1026s AC 1026s Processing line... 1026s GT 1026s GT 1026s Processing line... 1026s AC 1026s AC 1026s Processing line... 1026s AC 1026s AC 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s ACGGAC 1026s ACGGAC 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s CG 1026s CG 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s TGACAACCGAAAGACGGAC 1026s TGACAACCGAAAGACGGAC 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s CTGTTCACGTGG 1026s CTGTTCACGTGG 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s /usr/bin/bowtie2 --np 2 -D 26 -R 2 --rfg 6.63676579907774 --trim5 9 --score-min L,3.26575879267859,1.02716931575415 --cp-min 3 --mm --cp-ival 3 --rdg 20.1692331691202 --mp 5.07947885978767,2.84402674191737 -a --large-index --ma 34.1091081180024 -r -p 4 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1026s --- Summary --- 1026s Read 1 reference strings 1026s Checked 42 alignments, 0 edits 1026s --------------- 1026s PASSED 1026s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1026s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1026s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '2' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1026s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '6' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1026s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '7' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1026s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 1026s Warning: skipping read '11' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1026s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '34' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1026s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '35' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1026s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '38' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1026s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '39' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1026s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '18' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1026s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '19' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1026s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '22' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1026s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '23' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1026s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '27' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1026s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '30' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1026s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '31' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1026s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '42' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1026s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '47' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1026s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 1026s Warning: skipping read '49' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1026s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '52' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1026s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1026s Warning: skipping read '56' because it was < 2 characters long 1026s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1026s 58 reads; of these: 1026s 58 (100.00%) were unpaired; of these: 1026s 52 (89.66%) aligned 0 times 1026s 3 (5.17%) aligned exactly 1 time 1026s 3 (5.17%) aligned >1 times 1026s 10.34% overall alignment rate 1026s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1026s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1026s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1026s Flattened IUPAC characters 1026s Mutating sequence Sim.pm.2 1026s Introducing 10 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1026s Finished SNPs 1026s Finished ref gaps 1026s Finished read gaps 1026s Mutating sequence Sim.pm.1 1026s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1026s Finished SNPs 1026s Finished ref gaps 1026s Finished read gaps 1026s Mutated reference genome to subject genome 1026s SNPs introduced: 10 1026s Reference gaps introduced: 1 1026s Read gaps introduced: 1 1026s Rearrangements introduced: 0 1026s Created read sampler 1026s Sampling 88 reads 1026s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1026s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1026s parsing sequence Sim.pm.1... 1026s parsing sequence Sim.pm.2... 1026s Parsed 81 reference bases 1026s *** Run 52 of 100 1026s /usr/bin/bowtie2 --n-ceil 0.516364842136862,1.28540787625111 --gbar 3 --score-min L,9.98556227598935,1.5305167907355 -i S,0.230297269101845 -R 1 --np 2 --large-index --rdg 21.2172611767739,15.6967834142161 --local --mm --cp-ival 1 --cp-min 3 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1026s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1026s Warning: skipping read '10' because it was < 2 characters long 1026s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 1026s Warning: skipping read '26' because it was < 2 characters long 1026s 88 reads; of these: 1026s 88 (100.00%) were unpaired; of these: 1026s 88 (100.00%) aligned 0 times 1026s 0 (0.00%) aligned exactly 1 time 1026s 0 (0.00%) aligned >1 times 1026s 0.00% overall alignment rate 1026s Read 50 alignments... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s Processing line... 1026s --- Summary --- 1026s Read 1 reference strings 1026s Checked 0 alignments, 0 edits 1026s /usr/bin/bowtie2 --n-ceil 0.516364842136862,1.28540787625111 --gbar 3 --score-min L,9.98556227598935,1.5305167907355 -i S,0.230297269101845 -R 1 --np 2 --large-index --rdg 21.2172611767739,15.6967834142161 --local --mm --cp-ival 1 --cp-min 3 -r -p 2 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1026s --------------- 1026s PASSED 1026s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1026s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1026s Warning: skipping read '10' because it was < 2 characters long 1026s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 1026s Warning: skipping read '26' because it was < 2 characters long 1026s 88 reads; of these: 1026s 88 (100.00%) were unpaired; of these: 1026s 88 (100.00%) aligned 0 times 1026s 0 (0.00%) aligned exactly 1 time 1026s 0 (0.00%) aligned >1 times 1026s 0.00% overall alignment rate 1026s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1026s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1026s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1026s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1026s /usr/bin/bowtie2 --n-ceil 0.516364842136862,1.28540787625111 --gbar 3 --score-min L,9.98556227598935,1.5305167907355 -i S,0.230297269101845 -R 1 --np 2 --large-index --rdg 21.2172611767739,15.6967834142161 --local --mm --cp-ival 1 --cp-min 3 -r -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1027s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1027s Warning: skipping read '10' because it was < 2 characters long 1027s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 1027s Warning: skipping read '26' because it was < 2 characters long 1027s 88 reads; of these: 1027s 88 (100.00%) were unpaired; of these: 1027s 88 (100.00%) aligned 0 times 1027s 0 (0.00%) aligned exactly 1 time 1027s 0 (0.00%) aligned >1 times 1027s 0.00% overall alignment rate 1027s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1027s Flattened IUPAC characters 1027s Mutating sequence Sim.pm.1 1027s Introducing 16 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1027s Finished SNPs 1027s Finished ref gaps 1027s Finished read gaps 1027s Mutating sequence Sim.pm.2 1027s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1027s Finished SNPs 1027s Finished ref gaps 1027s Finished read gaps 1027s Mutated reference genome to subject genome 1027s SNPs introduced: 22 1027s Reference gaps introduced: 0 1027s Read gaps introduced: 0 1027s Rearrangements introduced: 1 1027s Created read sampler 1027s Sampling 84 reads 1027s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1027s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1027s parsing sequence Sim.pm.1... 1027s parsing sequence Sim.pm.2... 1027s Parsed 81 reference bases 1027s *** Run 53 of 100 1027s /usr/bin/bowtie2 -k 5 --large-index --ma 1.79939121610869 --rdg 41.4512512070855,5.4442777707072 --mp 8.10284348146138,5.19451391395819 --mm --cp-ival 1 --cp-min 2 --gbar 3 --score-min L,4.43670287501055,8.05031759584183 --n-ceil 0.809481653294498,1.43574392331682 --trim5 3 --norc --np 12 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1027s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1027s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '1' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1027s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '6' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1027s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '16' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1027s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 1027s Warning: skipping read '43' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1027s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '47' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1027s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 1027s Warning: skipping read '58' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1027s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '63' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1027s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 1027s Warning: skipping read '70' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1027s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '72' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1027s 84 reads; of these: 1027s 84 (100.00%) were unpaired; of these: 1027s 80 (95.24%) aligned 0 times 1027s 1 (1.19%) aligned exactly 1 time 1027s 3 (3.57%) aligned >1 times 1027s 4.76% overall alignment rate 1027s Read 50 alignments... 1027s Read 100 alignments... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s CC 1027s CC 1027s Processing line... 1027s CC 1027s CC 1027s Processing line... 1027s CC 1027s CC 1027s Processing line... 1027s CC 1027s CC 1027s Processing line... 1027s CC 1027s CC 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s ACCGAAAGACGG 1027s ACCGAAAGACGG 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s CC 1027s CC 1027s Processing line... 1027s CC 1027s CC 1027s Processing line... 1027s CC 1027s CC 1027s Processing line... 1027s CC 1027s CC 1027s Processing line... 1027s CC 1027s CC 1027s Processing line... 1027s TA 1027s TA 1027s Processing line... 1027s TA 1027s TA 1027s Processing line... 1027s TA 1027s TA 1027s Processing line... 1027s TA 1027s TA 1027s Processing line... 1027s TA 1027s TA 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s Processing line... 1027s --- Summary --- 1027s Read 1 reference strings 1027s Checked 16 alignments, 0 edits 1027s --------------- 1027s PASSED 1027s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1027s /usr/bin/bowtie2 -k 5 --large-index --ma 1.79939121610869 --rdg 41.4512512070855,5.4442777707072 --mp 8.10284348146138,5.19451391395819 --mm --cp-ival 1 --cp-min 2 --gbar 3 --score-min L,4.43670287501055,8.05031759584183 --n-ceil 0.809481653294498,1.43574392331682 --trim5 3 --norc --np 12 -q -p 2 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1027s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1027s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '1' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1027s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '6' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1027s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '16' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1027s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 1027s Warning: skipping read '43' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1027s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '47' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1027s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 1027s Warning: skipping read '70' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1027s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '72' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1027s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 1027s Warning: skipping read '58' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1027s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1027s Warning: skipping read '63' because it was < 2 characters long 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1027s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1027s 84 reads; of these: 1027s 84 (100.00%) were unpaired; of these: 1027s 80 (95.24%) aligned 0 times 1027s 1 (1.19%) aligned exactly 1 time 1027s 3 (3.57%) aligned >1 times 1027s 4.76% overall alignment rate 1027s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1027s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1027s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1027s Flattened IUPAC characters 1027s Mutating sequence Sim.pm.2 1027s Introducing 11 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1027s Finished SNPs 1027s Finished ref gaps 1027s Finished read gaps 1027s Mutating sequence Sim.pm.1 1027s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1027s Finished SNPs 1027s Finished ref gaps 1027s Finished read gaps 1027s Mutated reference genome to subject genome 1027s SNPs introduced: 19 1027s Reference gaps introduced: 0 1027s Read gaps introduced: 1 1027s Rearrangements introduced: 0 1027s Created read sampler 1027s Sampling 21 reads 1027s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1027s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1027s parsing sequence Sim.pm.1... 1027s parsing sequence Sim.pm.2... 1027s Parsed 81 reference bases 1027s *** Run 54 of 100 1027s /usr/bin/bowtie2 --rfg 17.321187096788,17.7835842592663 -i S,0.331610363529474 --local --trim5 3 --trim3 7 --score-min L,9.24153525639814,5.91446244052113 --large-index --np 5 --cp-min 4 --cp-ival 3 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1028s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '3' because it was < 2 characters long 1028s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '5' because it was < 2 characters long 1028s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '7' because it was < 2 characters long 1028s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '9' because it was < 2 characters long 1028s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '10' because it was < 2 characters long 1028s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '11' because it was < 2 characters long 1028s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '12' because it was < 2 characters long 1028s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '14' because it was < 2 characters long 1028s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '16' because it was < 2 characters long 1028s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '18' because it was < 2 characters long 1028s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '19' because it was < 2 characters long 1028s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 1028s Warning: skipping read '20' because it was < 2 characters long 1028s 21 reads; of these: 1028s 21 (100.00%) were unpaired; of these: 1028s 21 (100.00%) aligned 0 times 1028s 0 (0.00%) aligned exactly 1 time 1028s 0 (0.00%) aligned >1 times 1028s 0.00% overall alignment rate 1028s /usr/bin/bowtie2 --rfg 17.321187096788,17.7835842592663 -i S,0.331610363529474 --local --trim5 3 --trim3 7 --score-min L,9.24153525639814,5.91446244052113 --large-index --np 5 --cp-min 4 --cp-ival 3 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s --- Summary --- 1028s Read 1 reference strings 1028s Checked 0 alignments, 0 edits 1028s --------------- 1028s PASSED 1028s ALSO checking that bowtie2 and bowtie2-align match up 1028s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '3' because it was < 2 characters long 1028s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '5' because it was < 2 characters long 1028s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '7' because it was < 2 characters long 1028s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '9' because it was < 2 characters long 1028s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '10' because it was < 2 characters long 1028s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '11' because it was < 2 characters long 1028s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '12' because it was < 2 characters long 1028s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '14' because it was < 2 characters long 1028s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '16' because it was < 2 characters long 1028s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '18' because it was < 2 characters long 1028s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '19' because it was < 2 characters long 1028s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 1028s Warning: skipping read '20' because it was < 2 characters long 1028s 21 reads; of these: 1028s 21 (100.00%) were unpaired; of these: 1028s 21 (100.00%) aligned 0 times 1028s 0 (0.00%) aligned exactly 1 time 1028s 0 (0.00%) aligned >1 times 1028s 0.00% overall alignment rate 1028s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1028s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1028s /usr/bin/bowtie2 --rfg 17.321187096788,17.7835842592663 -i S,0.331610363529474 --local --trim5 3 --trim3 7 --score-min L,9.24153525639814,5.91446244052113 --large-index --np 5 --cp-min 4 --cp-ival 3 -q -p 3 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1028s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '3' because it was < 2 characters long 1028s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '5' because it was < 2 characters long 1028s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '7' because it was < 2 characters long 1028s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '9' because it was < 2 characters long 1028s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '10' because it was < 2 characters long 1028s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '11' because it was < 2 characters long 1028s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '12' because it was < 2 characters long 1028s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '14' because it was < 2 characters long 1028s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '16' because it was < 2 characters long 1028s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '18' because it was < 2 characters long 1028s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1028s Warning: skipping read '19' because it was < 2 characters long 1028s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 1028s Warning: skipping read '20' because it was < 2 characters long 1028s 21 reads; of these: 1028s 21 (100.00%) were unpaired; of these: 1028s 21 (100.00%) aligned 0 times 1028s 0 (0.00%) aligned exactly 1 time 1028s 0 (0.00%) aligned >1 times 1028s 0.00% overall alignment rate 1028s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1028s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1028s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1028s Flattened IUPAC characters 1028s Mutating sequence Sim.pm.2 1028s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1028s Finished SNPs 1028s Finished ref gaps 1028s Finished read gaps 1028s Mutating sequence Sim.pm.1 1028s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1028s Finished SNPs 1028s Finished ref gaps 1028s Finished read gaps 1028s Mutated reference genome to subject genome 1028s SNPs introduced: 6 1028s Reference gaps introduced: 0 1028s Read gaps introduced: 0 1028s Rearrangements introduced: 1 1028s Created read sampler 1028s Sampling 82 reads 1028s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1028s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1028s parsing sequence Sim.pm.1... 1028s *** Run 55 of 100 1028s /usr/bin/bowtie2 --cp-ival 5 -D 45 --cp-min 2 --score-min L,8.15382907077459,1.38552932709921 --gbar 1 --large-index --local -a -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1028s parsing sequence Sim.pm.2... 1028s Parsed 81 reference bases 1028s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 1028s Warning: skipping read '5' because it was < 2 characters long 1028s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 1028s Warning: skipping read '12' because it was < 2 characters long 1028s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 1028s Warning: skipping read '46' because it was < 2 characters long 1028s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 1028s Warning: skipping read '79' because it was < 2 characters long 1028s 82 reads; of these: 1028s 82 (100.00%) were unpaired; of these: 1028s 72 (87.80%) aligned 0 times 1028s 10 (12.20%) aligned exactly 1 time 1028s 0 (0.00%) aligned >1 times 1028s 12.20% overall alignment rate 1028s Read 50 alignments... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s TAGTGATGACAACCGAAAGACGGACGTA 1028s TAGNGATGACAACCGAAAGACGGACGTA 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s ATGACAACCGAAAGACGGACGTAAATCCC 1028s ATGACAACCGAAAGACGGACGTANATCCC 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s GATGACAACCGAAAGACGGACGTAAA 1028s GATGACAACCGAAAGACGGACGTANA 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s CTGTTCACGTGGGCGA 1028s CTGTTCACGTGGGCGA 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s ATCGCGTAGCGATGACAACCGAAAGACGGACGT 1028s ATCGCGTAGNGATGACAACCGAAAGACGGACGT 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s CAACCGAAAGACGGAC 1028s CAACCGAAAGACGGAC 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s GAAAGACGGACGTA 1028s GAAAGACGGACGTA 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s TGACAACCGAAA 1028s TGACAACCGAAA 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s TGACAACCGAAA 1028s TGACAACCGAAA 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s Processing line... 1028s CTCCTGTTCACGTG 1028s CTCCTGTTCACGTG 1028s Processing line... 1028s Processing line... 1028s --- Summary --- 1028s Read 1 reference strings 1028s Checked 10 alignments, 0 edits 1028s --------------- 1028s PASSED 1028s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1028s /usr/bin/bowtie2 --cp-ival 5 -D 45 --cp-min 2 --score-min L,8.15382907077459,1.38552932709921 --gbar 1 --large-index --local -a -q -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1029s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 1029s Warning: skipping read '5' because it was < 2 characters long 1029s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 1029s Warning: skipping read '12' because it was < 2 characters long 1029s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 1029s Warning: skipping read '46' because it was < 2 characters long 1029s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 1029s Warning: skipping read '79' because it was < 2 characters long 1029s 82 reads; of these: 1029s 82 (100.00%) were unpaired; of these: 1029s 72 (87.80%) aligned 0 times 1029s 10 (12.20%) aligned exactly 1 time 1029s 0 (0.00%) aligned >1 times 1029s 12.20% overall alignment rate 1029s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1029s Flattened IUPAC characters 1029s Mutating sequence Sim.pm.1 1029s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1029s Finished SNPs 1029s Finished ref gaps 1029s Finished read gaps 1029s Mutating sequence Sim.pm.2 1029s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1029s Finished SNPs 1029s Finished ref gaps 1029s Finished read gaps 1029s Mutated reference genome to subject genome 1029s SNPs introduced: 5 1029s Reference gaps introduced: 1 1029s Read gaps introduced: 0 1029s Rearrangements introduced: 0 1029s Created read sampler 1029s Sampling 135 reads 1029s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1029s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1029s parsing sequence Sim.pm.1... 1029s parsing sequence Sim.pm.2... 1029s Parsed 81 reference bases 1029s *** Run 56 of 100 1029s /usr/bin/bowtie2 --mp 9.13064338132026,3.34600719130161 --rfg 31.4589005508491 --local --large-index --score-min L,4.2929890835211,8.51997108021637 --cp-min 5 --np 3 --cp-ival 1 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1029s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 1029s Warning: skipping read '82' because it was < 2 characters long 1029s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 1029s Warning: skipping read '93' because it was < 2 characters long 1029s Warning: skipping read '103' because length (1) <= # seed mismatches (0) 1029s Warning: skipping read '103' because it was < 2 characters long 1029s Warning: skipping read '107' because length (1) <= # seed mismatches (0) 1029s Warning: skipping read '107' because it was < 2 characters long 1029s Warning: skipping read '114' because length (1) <= # seed mismatches (0) 1029s Warning: skipping read '114' because it was < 2 characters long 1029s Warning: skipping read '135' because length (1) <= # seed mismatches (0) 1029s Warning: skipping read '135' because it was < 2 characters long 1029s 135 reads; of these: 1029s 135 (100.00%) were unpaired; of these: 1029s 135 (100.00%) aligned 0 times 1029s 0 (0.00%) aligned exactly 1 time 1029s 0 (0.00%) aligned >1 times 1029s 0.00% overall alignment rate 1029s Read 50 alignments... 1029s Read 100 alignments... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s --- Summary --- 1029s Read 1 reference strings 1029s Checked 0 alignments, 0 edits 1029s --------------- 1029s PASSED 1029s Flattened IUPAC characters 1029s Mutating sequence Sim.pm.1 1029s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1029s Finished SNPs 1029s Finished ref gaps 1029s Finished read gaps 1029s Mutating sequence Sim.pm.2 1029s Introducing 9 SNPs, 0/3 ref/read gaps, and 0 rearrangements 1029s Finished SNPs 1029s Finished ref gaps 1029s Finished read gaps 1029s Mutated reference genome to subject genome 1029s SNPs introduced: 15 1029s Reference gaps introduced: 0 1029s Read gaps introduced: 3 1029s Rearrangements introduced: 0 1029s Created read sampler 1029s Sampling 72 reads 1029s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1029s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1029s parsing sequence Sim.pm.1... 1029s parsing sequence Sim.pm.2... 1029s Parsed 81 reference bases 1029s *** Run 57 of 100 1029s /usr/bin/bowtie2 --rfg 20.8134010667629 -i S,1.20533063749462 --local --mp 6.65028920503081,4.16824413058383 -k 2 --score-min L,6.90844767550847,3.88405690768028 --gbar 2 --large-index --cp-min 6 --cp-ival 1 --mm -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1029s 72 reads; of these: 1029s 72 (100.00%) were unpaired; of these: 1029s 72 (100.00%) aligned 0 times 1029s 0 (0.00%) aligned exactly 1 time 1029s 0 (0.00%) aligned >1 times 1029s 0.00% overall alignment rate 1029s Read 50 alignments... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s Processing line... 1029s --- Summary --- 1029s Read 1 reference strings 1029s Checked 0 alignments, 0 edits 1029s --------------- 1029s PASSED 1029s ALSO checking that bowtie2 and bowtie2-align match up 1029s /usr/bin/bowtie2 --rfg 20.8134010667629 -i S,1.20533063749462 --local --mp 6.65028920503081,4.16824413058383 -k 2 --score-min L,6.90844767550847,3.88405690768028 --gbar 2 --large-index --cp-min 6 --cp-ival 1 --mm -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1029s 72 reads; of these: 1029s 72 (100.00%) were unpaired; of these: 1029s 72 (100.00%) aligned 0 times 1029s 0 (0.00%) aligned exactly 1 time 1029s 0 (0.00%) aligned >1 times 1029s 0.00% overall alignment rate 1029s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1029s Flattened IUPAC characters 1029s Mutating sequence Sim.pm.2 1029s Introducing 9 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1029s Finished SNPs 1029s Finished ref gaps 1029s Finished read gaps 1029s Mutating sequence Sim.pm.1 1029s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1029s Finished SNPs 1029s Finished ref gaps 1030s Finished read gaps 1030s Mutated reference genome to subject genome 1030s SNPs introduced: 16 1030s Reference gaps introduced: 0 1030s Read gaps introduced: 1 1030s Rearrangements introduced: 0 1030s Created read sampler 1030s Sampling 120 reads 1030s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1030s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1030s parsing sequence Sim.pm.1... 1030s *** Run 58 of 100 1030s /usr/bin/bowtie2 -k 5 --large-index --local --mp 8.25746139599207,7.0218705166406 --rdg 45.5426175995369,13.4769940439353 --cp-ival 2 --cp-min 7 --score-min L,3.58354434352427,1.44031588333978 --rfg 21.5546694081961,10.2620932246921 -i C,1.88386638887629 -R 4 -N 0 -L21 --np 2 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1030s parsing sequence Sim.pm.2... 1030s Parsed 81 reference bases 1030s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 1030s Warning: skipping read '19' because it was < 2 characters long 1030s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 1030s Warning: skipping read '21' because it was < 2 characters long 1030s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1030s Warning: skipping read '22' because it was < 2 characters long 1030s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 1030s Warning: skipping read '34' because it was < 2 characters long 1030s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 1030s Warning: skipping read '44' because it was < 2 characters long 1030s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1030s Warning: skipping read '56' because it was < 2 characters long 1030s 120 reads; of these: 1030s 120 (100.00%) were unpaired; of these: 1030s 107 (89.17%) aligned 0 times 1030s 10 (8.33%) aligned exactly 1 time 1030s 3 (2.50%) aligned >1 times 1030s 10.83% overall alignment rate 1030s Read 50 alignments... 1030s Read 100 alignments... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s AACCGAAAGACGG 1030s AACCGAAAGACGG 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s CCTGTTCACGTGG 1030s CCTGTTCACGTGG 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s GATGACAAC 1030s GATGACAAC 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s CTGTTCACGTGGGCGA 1030s CTGTTCACGTGGGCGA 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s GGGCG 1030s GGGCG 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s TCCCG 1030s TCCCG 1030s Processing line... 1030s TCCCG 1030s TCCCG 1030s Processing line... 1030s Processing line... 1030s TCCCGTATCGCGTAG 1030s TCCCGTATCGCGTAG 1030s Processing line... 1030s TCCCGTATCGCGTAG 1030s TCCCGTATCGCGTAG 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s ACAACCGAA 1030s ACAACCGAA 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s GATGACAACCGAAAGACGGACGTAGATCCCGTATCGCGTA 1030s GATGACAACCGAAAGACGGACGTANATCCCGTATCGCGTA 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s ACAACCGAAAGA 1030s ACAACCGAAAGA 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s ATCCCGTATCGCGTA 1030s ATCCCGTATCGCGTA 1030s Processing line... 1030s ATCCCGTATCGCGTA 1030s ATCCCGTATCGCGTA 1030s Processing line... 1030s Processing line... 1030s GACGGACG 1030s GACGGACG 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s CCGAA 1030s CCGAA 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s --- Summary --- 1030s Read 1 reference strings 1030s Checked 16 alignments, 0 edits 1030s --------------- 1030s PASSED 1030s Flattened IUPAC characters 1030s Mutating sequence Sim.pm.1 1030s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1030s Finished SNPs 1030s Finished ref gaps 1030s Finished read gaps 1030s Mutating sequence Sim.pm.2 1030s Introducing 2 SNPs, 0/3 ref/read gaps, and 0 rearrangements 1030s Finished SNPs 1030s Finished ref gaps 1030s Finished read gaps 1030s Mutated reference genome to subject genome 1030s SNPs introduced: 4 1030s Reference gaps introduced: 0 1030s Read gaps introduced: 3 1030s Rearrangements introduced: 0 1030s Created read sampler 1030s Sampling 111 reads 1030s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1030s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1030s parsing sequence Sim.pm.1... 1030s parsing sequence Sim.pm.2... 1030s *** Run 59 of 100 1030s /usr/bin/bowtie2 --ma 27.1151287419656 --large-index --mp 8.9160891444737,3.68997332437324 --rdg 2.58378667692741 --cp-ival 1 --cp-min 2 --n-ceil 0.758467071675556,1.40380364555088 --score-min L,2.11263788518227,1.38819172559134 -i L,0.461730949230087 --norc -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1030s Parsed 81 reference bases 1030s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1030s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 1030s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1030s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 1030s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1030s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 1030s Warning: skipping mate #2 of read '53' because it was < 2 characters long 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1030s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 1030s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1030s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 1030s Warning: skipping mate #1 of read '64' because it was < 2 characters long 1030s Read 50 alignments... 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1030s Read 100 alignments... 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1030s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1030s 111 reads; of these: 1030s 111 (100.00%) were paired; of these: 1030s 110 (99.10%) aligned concordantly 0 times 1030s 0 (0.00%) aligned concordantly exactly 1 time 1030s 1 (0.90%) aligned concordantly >1 times 1030s ---- 1030s 110 pairs aligned concordantly 0 times; of these: 1030s 0 (0.00%) aligned discordantly 1 time 1030s ---- 1030s 110 pairs aligned 0 times concordantly or discordantly; of these: 1030s 220 mates make up the pairs; of these: 1030s 208 (94.55%) aligned 0 times 1030s 4 (1.82%) aligned exactly 1 time 1030s 8 (3.64%) aligned >1 times 1030s 6.31% overall alignment rate 1030s Read 150 alignments... 1030s Read 200 alignments... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s TCCCG 1030s TCCCG 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s AGA 1030s AGA 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s TGACAACCGAAAGA 1030s TGACAACCGAAAGA 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s /usr/bin/bowtie2 --ma 27.1151287419656 --large-index --mp 8.9160891444737,3.68997332437324 --rdg 2.58378667692741 --cp-ival 1 --cp-min 2 --n-ceil 0.758467071675556,1.40380364555088 --score-min L,2.11263788518227,1.38819172559134 -i L,0.461730949230087 --norc -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s CGTATCGCGTAG 1030s CGTATCGCGTAG 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s ACG 1030s ACG 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s CGT 1030s CGT 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s ATGACAACCG 1030s ATGACAACCG 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s CCGAAAGACGGAC 1030s CCGAAAGACGGAC 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s AC 1030s AC 1030s Processing line... 1030s Processing line... 1030s GG 1030s GG 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s AT 1030s AT 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s CC 1030s CC 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s GGACGT 1030s GGACGT 1030s Processing line... 1030s ATCGCGT 1030s ATCGCGT 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s Processing line... 1030s --- Summary --- 1030s Read 1 reference strings 1030s Checked 14 alignments, 0 edits 1030s --------------- 1030s PASSED 1030s ALSO checking that bowtie2 and bowtie2-align match up 1031s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1031s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 1031s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1031s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 1031s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1031s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 1031s Warning: skipping mate #2 of read '53' because it was < 2 characters long 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1031s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 1031s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1031s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 1031s Warning: skipping mate #1 of read '64' because it was < 2 characters long 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1031s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1031s 111 reads; of these: 1031s 111 (100.00%) were paired; of these: 1031s 110 (99.10%) aligned concordantly 0 times 1031s 0 (0.00%) aligned concordantly exactly 1 time 1031s 1 (0.90%) aligned concordantly >1 times 1031s ---- 1031s 110 pairs aligned concordantly 0 times; of these: 1031s 0 (0.00%) aligned discordantly 1 time 1031s ---- 1031s 110 pairs aligned 0 times concordantly or discordantly; of these: 1031s 220 mates make up the pairs; of these: 1031s 208 (94.55%) aligned 0 times 1031s 4 (1.82%) aligned exactly 1 time 1031s 8 (3.64%) aligned >1 times 1031s 6.31% overall alignment rate 1031s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1031s Flattened IUPAC characters 1031s Mutating sequence Sim.pm.1 1031s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1031s Finished SNPs 1031s Finished ref gaps 1031s Finished read gaps 1031s Mutating sequence Sim.pm.2 1031s Introducing 2 SNPs, 1/2 ref/read gaps, and 1 rearrangements 1031s Finished SNPs 1031s Finished ref gaps 1031s Finished read gaps 1031s Mutated reference genome to subject genome 1031s SNPs introduced: 9 1031s Reference gaps introduced: 2 1031s Read gaps introduced: 2 1031s Rearrangements introduced: 1 1031s Created read sampler 1031s Sampling 42 reads 1031s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1031s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1031s *** Run 60 of 100 1031s /usr/bin/bowtie2 --large-index -M 3 --local --rdg 48.2028148529303,6.32823349391103 --cp-ival 1 --mm --cp-min 2 --score-min L,5.81044937990988,3.20194446116932 --gbar 1 --rfg 40.0054070090221 -i L,0.00190390863541152 --trim5 0 -N 0 -L22 --norc -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1031s parsing sequence Sim.pm.1... 1031s parsing sequence Sim.pm.2... 1031s Parsed 81 reference bases 1031s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1031s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 1031s Warning: skipping mate #2 of read '26' because it was < 2 characters long 1031s 42 reads; of these: 1031s 42 (100.00%) were paired; of these: 1031s 42 (100.00%) aligned concordantly 0 times 1031s 0 (0.00%) aligned concordantly exactly 1 time 1031s 0 (0.00%) aligned concordantly >1 times 1031s ---- 1031s 42 pairs aligned concordantly 0 times; of these: 1031s 0 (0.00%) aligned discordantly 1 time 1031s ---- 1031s 42 pairs aligned 0 times concordantly or discordantly; of these: 1031s 84 mates make up the pairs; of these: 1031s 84 (100.00%) aligned 0 times 1031s 0 (0.00%) aligned exactly 1 time 1031s 0 (0.00%) aligned >1 times 1031s 0.00% overall alignment rate 1031s Read 50 alignments... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s Processing line... 1031s --- Summary --- 1031s Read 1 reference strings 1031s Checked 0 alignments, 0 edits 1031s --------------- 1031s PASSED 1031s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1031s /usr/bin/bowtie2 --large-index -M 3 --local --rdg 48.2028148529303,6.32823349391103 --cp-ival 1 --mm --cp-min 2 --score-min L,5.81044937990988,3.20194446116932 --gbar 1 --rfg 40.0054070090221 -i L,0.00190390863541152 --trim5 0 -N 0 -L22 --norc -q -p 3 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1031s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1031s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 1031s Warning: skipping mate #2 of read '26' because it was < 2 characters long 1031s 42 reads; of these: 1031s 42 (100.00%) were paired; of these: 1031s 42 (100.00%) aligned concordantly 0 times 1031s 0 (0.00%) aligned concordantly exactly 1 time 1031s 0 (0.00%) aligned concordantly >1 times 1031s ---- 1031s 42 pairs aligned concordantly 0 times; of these: 1031s 0 (0.00%) aligned discordantly 1 time 1031s ---- 1031s 42 pairs aligned 0 times concordantly or discordantly; of these: 1031s 84 mates make up the pairs; of these: 1031s 84 (100.00%) aligned 0 times 1031s 0 (0.00%) aligned exactly 1 time 1031s 0 (0.00%) aligned >1 times 1031s 0.00% overall alignment rate 1031s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1031s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1031s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1031s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1031s /usr/bin/bowtie2 --large-index -M 3 --local --rdg 48.2028148529303,6.32823349391103 --cp-ival 1 --mm --cp-min 2 --score-min L,5.81044937990988,3.20194446116932 --gbar 1 --rfg 40.0054070090221 -i L,0.00190390863541152 --trim5 0 -N 0 -L22 --norc -q -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1031s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1031s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 1031s Warning: skipping mate #2 of read '26' because it was < 2 characters long 1031s 42 reads; of these: 1031s 42 (100.00%) were paired; of these: 1031s 42 (100.00%) aligned concordantly 0 times 1031s 0 (0.00%) aligned concordantly exactly 1 time 1031s 0 (0.00%) aligned concordantly >1 times 1031s ---- 1031s 42 pairs aligned concordantly 0 times; of these: 1031s 0 (0.00%) aligned discordantly 1 time 1031s ---- 1031s 42 pairs aligned 0 times concordantly or discordantly; of these: 1031s 84 mates make up the pairs; of these: 1031s 84 (100.00%) aligned 0 times 1031s 0 (0.00%) aligned exactly 1 time 1031s 0 (0.00%) aligned >1 times 1031s 0.00% overall alignment rate 1031s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1031s Flattened IUPAC characters 1031s Mutating sequence Sim.pm.2 1031s Introducing 8 SNPs, 0/3 ref/read gaps, and 0 rearrangements 1031s Finished SNPs 1031s Finished ref gaps 1031s Finished read gaps 1031s Mutating sequence Sim.pm.1 1031s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1031s Finished SNPs 1031s Finished ref gaps 1031s Finished read gaps 1031s Mutated reference genome to subject genome 1031s SNPs introduced: 8 1031s Reference gaps introduced: 0 1031s Read gaps introduced: 3 1031s Rearrangements introduced: 0 1031s Created read sampler 1031s Sampling 43 reads 1031s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1031s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1031s parsing sequence Sim.pm.1... 1031s *** Run 61 of 100 1031s /usr/bin/bowtie2 --cp-min 5 --mm --cp-ival 2 --rdg 11.7447099673098,5.82800608797954 --mp 8.4011540986123,7.866873556601 -a --trim3 4 --large-index --np 1 -N 1 -L25 -i C,1.52832688759444 --rfg 39.5800325513365,2.51056125825164 --score-min L,8.04350910135465,6.01286278157185 -f -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta 1031s parsing sequence Sim.pm.2... 1031s Parsed 81 reference bases 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1032s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1032s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1032s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1032s Warning: skipping mate #2 of read '5' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1032s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1032s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '11' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1032s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1032s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1032s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1032s 43 reads; of these: 1032s 37 (86.05%) were paired; of these: 1032s 37 (100.00%) aligned concordantly 0 times 1032s 0 (0.00%) aligned concordantly exactly 1 time 1032s 0 (0.00%) aligned concordantly >1 times 1032s ---- 1032s 37 pairs aligned concordantly 0 times; of these: 1032s 0 (0.00%) aligned discordantly 1 time 1032s ---- 1032s 37 pairs aligned 0 times concordantly or discordantly; of these: 1032s 74 mates make up the pairs; of these: 1032s 67 (90.54%) aligned 0 times 1032s 2 (2.70%) aligned exactly 1 time 1032s 5 (6.76%) aligned >1 times 1032s 6 (13.95%) were unpaired; of these: 1032s 6 (100.00%) aligned 0 times 1032s 0 (0.00%) aligned exactly 1 time 1032s 0 (0.00%) aligned >1 times 1032s 8.75% overall alignment rate 1032s Read 50 alignments... 1032s Read 100 alignments... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s CG 1032s CG 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s GAC 1032s GAC 1032s Processing line... 1032s GAC 1032s GAC 1032s Processing line... 1032s GAC 1032s GAC 1032s Processing line... 1032s GAC 1032s GAC 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s GAAAGA 1032s GAAAGA 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s GTA 1032s GTA 1032s Processing line... 1032s GTA 1032s GTA 1032s Processing line... 1032s GTA 1032s GTA 1032s Processing line... 1032s GTA 1032s GTA 1032s Processing line... 1032s GTA 1032s GTA 1032s Processing line... 1032s Processing line... 1032s GT 1032s GT 1032s Processing line... 1032s GT 1032s GT 1032s Processing line... 1032s AC 1032s AC 1032s Processing line... 1032s GT 1032s GT 1032s Processing line... 1032s GT 1032s GT 1032s Processing line... 1032s GT 1032s GT 1032s Processing line... 1032s AC 1032s AC 1032s Processing line... 1032s GT 1032s GT 1032s Processing line... 1032s AC 1032s AC 1032s Processing line... 1032s AC 1032s AC 1032s Processing line... 1032s GT 1032s GT 1032s Processing line... 1032s AC 1032s AC 1032s Processing line... 1032s AC 1032s AC 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s TGACAA 1032s TGACAA 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s ATCCCGTATCGCGTA 1032s ATCCCGTATCGCGTA 1032s Processing line... 1032s ATCCCGTATCGCGTA 1032s ATCCCGTATCGCGTA 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s Processing line... 1032s --- Summary --- 1032s Read 1 reference strings 1032s Checked 50 alignments, 0 edits 1032s --------------- 1032s PASSED 1032s ALSO checking that bowtie2 and bowtie2-align match up 1032s /usr/bin/bowtie2 --cp-min 5 --mm --cp-ival 2 --rdg 11.7447099673098,5.82800608797954 --mp 8.4011540986123,7.866873556601 -a --trim3 4 --large-index --np 1 -N 1 -L25 -i C,1.52832688759444 --rfg 39.5800325513365,2.51056125825164 --score-min L,8.04350910135465,6.01286278157185 -f -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1032s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1032s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1032s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1032s Warning: skipping mate #2 of read '5' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1032s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1032s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (1) 1032s Warning: skipping mate #1 of read '11' because it was < 2 characters long 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1032s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1033s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (1) 1033s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1033s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (1) 1033s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1033s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (1) 1033s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1033s 43 reads; of these: 1033s 37 (86.05%) were paired; of these: 1033s 37 (100.00%) aligned concordantly 0 times 1033s 0 (0.00%) aligned concordantly exactly 1 time 1033s 0 (0.00%) aligned concordantly >1 times 1033s ---- 1033s 37 pairs aligned concordantly 0 times; of these: 1033s 0 (0.00%) aligned discordantly 1 time 1033s ---- 1033s 37 pairs aligned 0 times concordantly or discordantly; of these: 1033s 74 mates make up the pairs; of these: 1033s 67 (90.54%) aligned 0 times 1033s 2 (2.70%) aligned exactly 1 time 1033s 5 (6.76%) aligned >1 times 1033s 6 (13.95%) were unpaired; of these: 1033s 6 (100.00%) aligned 0 times 1033s 0 (0.00%) aligned exactly 1 time 1033s 0 (0.00%) aligned >1 times 1033s 8.75% overall alignment rate 1033s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1033s Flattened IUPAC characters 1033s Mutating sequence Sim.pm.2 1033s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1033s Finished SNPs 1033s Finished ref gaps 1033s Finished read gaps 1033s Mutating sequence Sim.pm.1 1033s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1033s Finished SNPs 1033s Finished ref gaps 1033s Finished read gaps 1033s Mutated reference genome to subject genome 1033s SNPs introduced: 12 1033s Reference gaps introduced: 1 1033s Read gaps introduced: 0 1033s Rearrangements introduced: 1 1033s Created read sampler 1033s Sampling 37 reads 1033s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1033s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1033s parsing sequence Sim.pm.1... 1033s parsing sequence Sim.pm.2... 1033s Parsed 81 reference bases 1033s *** Run 62 of 100 1033s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 3 --large-index --local --rdg 33.4131774549,6.59619208037682 -R 4 -N 0 -L24 --norc --nofw --np 2 --gbar 1 --score-min L,7.24879834155918,3.31049773487836 --rfg 12.8748851015071,5.56714758379736 --trim5 5 -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta 1033s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read '4' because it was < 2 characters long 1033s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read '5' because it was < 2 characters long 1033s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read '14' because it was < 2 characters long 1033s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read '15' because it was < 2 characters long 1033s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read '23' because it was < 2 characters long 1033s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read '26' because it was < 2 characters long 1033s 37 reads; of these: 1033s 37 (100.00%) were unpaired; of these: 1033s 37 (100.00%) aligned 0 times 1033s 0 (0.00%) aligned exactly 1 time 1033s 0 (0.00%) aligned >1 times 1033s 0.00% overall alignment rate 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s --- Summary --- 1033s Read 1 reference strings 1033s Checked 0 alignments, 0 edits 1033s --------------- 1033s PASSED 1033s Flattened IUPAC characters 1033s Mutating sequence Sim.pm.1 1033s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1033s Finished SNPs 1033s Finished ref gaps 1033s Finished read gaps 1033s Mutating sequence Sim.pm.2 1033s Introducing 9 SNPs, 3/0 ref/read gaps, and 1 rearrangements 1033s Finished SNPs 1033s Finished ref gaps 1033s Finished read gaps 1033s Mutated reference genome to subject genome 1033s SNPs introduced: 13 1033s Reference gaps introduced: 4 1033s Read gaps introduced: 0 1033s Rearrangements introduced: 1 1033s Created read sampler 1033s Sampling 97 reads 1033s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1033s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1033s parsing sequence Sim.pm.1... 1033s parsing sequence Sim.pm.2... 1033s Parsed 81 reference bases 1033s *** Run 63 of 100 1033s /usr/bin/bowtie2 --cp-min 3 --nofw --np 2 --cp-ival 1 --mm --trim3 7 --rdg 40.316039222229 --rfg 37.0719507616553 --large-index --score-min L,5.30908688217047,5.15660647037977 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1033s 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 1033s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1033s 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 1033s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 1033s 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 1033s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1033s 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 1033s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1033s 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 1033s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 1033s 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 1033s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 1033s 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 1033s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1033s 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 1033s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 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 1033s 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 1033s 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 1033s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 1033s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1033s 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 1033s 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 1033s 97 reads; of these: 1033s 97 (100.00%) were unpaired; of these: 1033s 85 (87.63%) aligned 0 times 1033s 1 (1.03%) aligned exactly 1 time 1033s 11 (11.34%) aligned >1 times 1033s 12.37% overall alignment rate 1033s Read 50 alignments... 1033s Read 100 alignments... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s CGTATCGCGTA 1033s CGTATCGCGTA 1033s Processing line... 1033s GT 1033s GT 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s GTATCG 1033s GTATCG 1033s Processing line... 1033s Processing line... 1033s TA 1033s TA 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s AC 1033s AC 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s GGC 1033s GGC 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s CCGTAT 1033s CCGTAT 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s CGTATCGCGTA 1033s CGTATCGCGTA 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s CGCG 1033s CGCG 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s CGCG 1033s CGCG 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s CG 1033s CG 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s CA 1033s CA 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s Processing line... 1033s --- Summary --- 1033s Read 1 reference strings 1033s Checked 12 alignments, 0 edits 1033s --------------- 1033s PASSED 1033s *** Run 64 of 100 1033s /usr/bin/bowtie2 -D 14 --np 2 --score-min L,3.0887439081181,6.91289355028232 --trim5 2 --cp-ival 1 --cp-min 3 -M 4 --large-index --ma 12.1261545674517 --rdg 27.3645966458091 -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta 1033s Flattened IUPAC characters 1033s Mutating sequence Sim.pm.2 1033s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1033s Finished SNPs 1033s Finished ref gaps 1033s Finished read gaps 1033s Mutating sequence Sim.pm.1 1033s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1033s Finished SNPs 1033s Finished ref gaps 1033s Finished read gaps 1033s Mutated reference genome to subject genome 1033s SNPs introduced: 8 1033s Reference gaps introduced: 0 1033s Read gaps introduced: 0 1033s Rearrangements introduced: 2 1033s Created read sampler 1033s Sampling 47 reads 1033s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1033s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1033s parsing sequence Sim.pm.1... 1033s parsing sequence Sim.pm.2... 1033s Parsed 81 reference bases 1033s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1033s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1033s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 1033s Warning: skipping read '3' because it was < 2 characters long 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1033s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1033s 47 reads; of these: 1033s 47 (100.00%) were unpaired; of these: 1033s 41 (87.23%) aligned 0 times 1033s 4 (8.51%) aligned exactly 1 time 1033s 2 (4.26%) aligned >1 times 1033s 12.77% overall alignment rate 1033s Read 50 alignments... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s CACG 1034s CACG 1034s Processing line... 1034s AAGACGGACG 1034s AAGACGGACG 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s GAAA 1034s GAAA 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s GTATCG 1034s GTATCG 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s TTCACG 1034s TTCACG 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s CACGTGG 1034s CACGTGG 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s Processing line... 1034s --- Summary --- 1034s Read 1 reference strings 1034s Checked 6 alignments, 0 edits 1034s --------------- 1034s /usr/bin/bowtie2 -D 14 --np 2 --score-min L,3.0887439081181,6.91289355028232 --trim5 2 --cp-ival 1 --cp-min 3 -M 4 --large-index --ma 12.1261545674517 --rdg 27.3645966458091 -f -p 4 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1034s PASSED 1034s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1034s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1034s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1034s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 1034s Warning: skipping read '3' because it was < 2 characters long 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1034s 47 reads; of these: 1034s 47 (100.00%) were unpaired; of these: 1034s 41 (87.23%) aligned 0 times 1034s 4 (8.51%) aligned exactly 1 time 1034s 2 (4.26%) aligned >1 times 1034s 12.77% overall alignment rate 1034s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1034s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1034s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1034s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1034s /usr/bin/bowtie2 -D 14 --np 2 --score-min L,3.0887439081181,6.91289355028232 --trim5 2 --cp-ival 1 --cp-min 3 -M 4 --large-index --ma 12.1261545674517 --rdg 27.3645966458091 -f -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1034s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1034s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1034s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 1034s Warning: skipping read '3' because it was < 2 characters long 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1034s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1034s 47 reads; of these: 1034s 47 (100.00%) were unpaired; of these: 1034s 41 (87.23%) aligned 0 times 1034s 4 (8.51%) aligned exactly 1 time 1034s 2 (4.26%) aligned >1 times 1034s 12.77% overall alignment rate 1034s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1034s Flattened IUPAC characters 1034s Mutating sequence Sim.pm.2 1034s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1034s Finished SNPs 1034s Finished ref gaps 1034s Finished read gaps 1034s Mutating sequence Sim.pm.1 1034s *** Run 65 of 100 1034s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 3 -k 3 --large-index --local --trim3 8 -D 5 -N 1 -L23 --np 3 --score-min L,1.64775235022369,2.80315785448459 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1034s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1034s Finished SNPs 1034s Finished ref gaps 1034s Finished read gaps 1034s Mutated reference genome to subject genome 1034s SNPs introduced: 9 1034s Reference gaps introduced: 0 1034s Read gaps introduced: 1 1034s Rearrangements introduced: 0 1034s Created read sampler 1034s Sampling 122 reads 1034s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1034s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1034s parsing sequence Sim.pm.1... 1034s parsing sequence Sim.pm.2... 1034s Parsed 81 reference bases 1034s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '14' because it was < 2 characters long 1034s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '17' because it was < 2 characters long 1034s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '18' because it was < 2 characters long 1034s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '26' because it was < 2 characters long 1034s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '33' because it was < 2 characters long 1034s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '38' because it was < 2 characters long 1034s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '46' because it was < 2 characters long 1034s Warning: skipping read '57' because length (1) <= # seed mismatches (1) 1034s Warning: skipping read '57' because it was < 2 characters long 1034s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '63' because it was < 2 characters long 1034s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '65' because it was < 2 characters long 1034s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '68' because it was < 2 characters long 1034s Warning: skipping read '69' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '69' because it was < 2 characters long 1034s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '70' because it was < 2 characters long 1034s Warning: skipping read '72' because length (1) <= # seed mismatches (1) 1034s Warning: skipping read '72' because it was < 2 characters long 1034s Warning: skipping read '74' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '74' because it was < 2 characters long 1034s Warning: skipping read '78' because length (1) <= # seed mismatches (1) 1034s Warning: skipping read '78' because it was < 2 characters long 1034s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '80' because it was < 2 characters long 1034s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '81' because it was < 2 characters long 1034s Warning: skipping read '84' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '84' because it was < 2 characters long 1034s Warning: skipping read '86' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '86' because it was < 2 characters long 1034s Warning: skipping read '90' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '90' because it was < 2 characters long 1034s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '91' because it was < 2 characters long 1034s Warning: skipping read '92' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '92' because it was < 2 characters long 1034s Warning: skipping read '93' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '93' because it was < 2 characters long 1034s Warning: skipping read '98' because length (1) <= # seed mismatches (1) 1034s Warning: skipping read '98' because it was < 2 characters long 1034s Warning: skipping read '107' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '107' because it was < 2 characters long 1034s Warning: skipping read '116' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '116' because it was < 2 characters long 1034s Warning: skipping read '117' because length (1) <= # seed mismatches (1) 1034s Warning: skipping read '117' because it was < 2 characters long 1034s Warning: skipping read '121' because length (0) <= # seed mismatches (1) 1034s Warning: skipping read '121' because it was < 2 characters long 1035s 122 reads; of these: 1035s 122 (100.00%) were unpaired; of these: 1035s 122 (100.00%) aligned 0 times 1035s 0 (0.00%) aligned exactly 1 time 1035s 0 (0.00%) aligned >1 times 1035s 0.00% overall alignment rate 1035s Read 50 alignments... 1035s Read 100 alignments... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s --- Summary --- 1035s Read 1 reference strings 1035s Checked 0 alignments, 0 edits 1035s --------------- 1035s PASSED 1035s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1035s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 3 -k 3 --large-index --local --trim3 8 -D 5 -N 1 -L23 --np 3 --score-min L,1.64775235022369,2.80315785448459 -q -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1035s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '14' because it was < 2 characters long 1035s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '17' because it was < 2 characters long 1035s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '18' because it was < 2 characters long 1035s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '26' because it was < 2 characters long 1035s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '33' because it was < 2 characters long 1035s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '38' because it was < 2 characters long 1035s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '46' because it was < 2 characters long 1035s Warning: skipping read '57' because length (1) <= # seed mismatches (1) 1035s Warning: skipping read '57' because it was < 2 characters long 1035s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '63' because it was < 2 characters long 1035s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '65' because it was < 2 characters long 1035s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '68' because it was < 2 characters long 1035s Warning: skipping read '69' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '69' because it was < 2 characters long 1035s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '70' because it was < 2 characters long 1035s Warning: skipping read '72' because length (1) <= # seed mismatches (1) 1035s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '81' because it was < 2 characters long 1035s Warning: skipping read '84' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '84' because it was < 2 characters long 1035s Warning: skipping read '86' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '86' because it was < 2 characters long 1035s Warning: skipping read '90' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '90' because it was < 2 characters long 1035s Warning: skipping read '72' because it was < 2 characters long 1035s Warning: skipping read '74' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '98' because length (1) <= # seed mismatches (1) 1035s Warning: skipping read '98' because it was < 2 characters long 1035s Warning: skipping read '107' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '107' because it was < 2 characters long 1035s Warning: skipping read '74' because it was < 2 characters long 1035s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '91' because it was < 2 characters long 1035s Warning: skipping read '92' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '92' because it was < 2 characters long 1035s Warning: skipping read '93' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '93' because it was < 2 characters long 1035s Warning: skipping read '78' because length (1) <= # seed mismatches (1) 1035s Warning: skipping read '78' because it was < 2 characters long 1035s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '80' because it was < 2 characters long 1035s Warning: skipping read '116' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '116' because it was < 2 characters long 1035s Warning: skipping read '117' because length (1) <= # seed mismatches (1) 1035s Warning: skipping read '117' because it was < 2 characters long 1035s Warning: skipping read '121' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read '121' because it was < 2 characters long 1035s 122 reads; of these: 1035s 122 (100.00%) were unpaired; of these: 1035s 122 (100.00%) aligned 0 times 1035s 0 (0.00%) aligned exactly 1 time 1035s 0 (0.00%) aligned >1 times 1035s 0.00% overall alignment rate 1035s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1035s Flattened IUPAC characters 1035s Mutating sequence Sim.pm.2 1035s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1035s Finished SNPs 1035s Finished ref gaps 1035s Finished read gaps 1035s Mutating sequence Sim.pm.1 1035s Introducing 3 SNPs, 1/2 ref/read gaps, and 0 rearrangements 1035s Finished SNPs 1035s Finished ref gaps 1035s Finished read gaps 1035s Mutated reference genome to subject genome 1035s SNPs introduced: 7 1035s Reference gaps introduced: 1 1035s Read gaps introduced: 3 1035s Rearrangements introduced: 1 1035s Created read sampler 1035s Sampling 50 reads 1035s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1035s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1035s parsing sequence Sim.pm.1... 1035s parsing sequence Sim.pm.2... 1035s Parsed 81 reference bases 1035s *** Run 66 of 100 1035s /usr/bin/bowtie2 --score-min L,5.1258097350103,2.32489180500424 --rfg 10.7750791143075,16.7172352354811 -N 1 -L13 -D 12 -R 4 --np 5 --large-index --trim3 9 --mp 7.53956975921217,5.74552065756603 --cp-ival 1 --mm --cp-min 3 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1035s 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 1035s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1035s 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 1035s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1035s 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 1035s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1035s 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 1035s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1035s 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 1035s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s 50 reads; of these: 1035s 50 (100.00%) were unpaired; of these: 1035s 43 (86.00%) aligned 0 times 1035s 2 (4.00%) aligned exactly 1 time 1035s 5 (10.00%) aligned >1 times 1035s 14.00% overall alignment rate 1035s Read 50 alignments... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s GACG 1035s GACG 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s ATCG 1035s ATCG 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s TGT 1035s TGT 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s GACAACC 1035s GACAACC 1035s Processing line... 1035s Processing line... 1035s CGAAAG 1035s CGAAAG 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s Processing line... 1035s TATC 1035s TATC 1035s Processing line... 1035s Processing line... 1035s GTATCGCG 1035s GTATCGCG 1035s Processing line... 1035s Processing line... 1035s --- Summary --- 1035s Read 1 reference strings 1035s Checked 7 alignments, 0 edits 1035s --------------- 1035s PASSED 1035s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1035s /usr/bin/bowtie2 --score-min L,5.1258097350103,2.32489180500424 --rfg 10.7750791143075,16.7172352354811 -N 1 -L13 -D 12 -R 4 --np 5 --large-index --trim3 9 --mp 7.53956975921217,5.74552065756603 --cp-ival 1 --mm --cp-min 3 --qseq -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1035s 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 1035s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1035s 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 1035s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1035s 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 1035s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1035s 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 1035s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1035s 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 1035s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1035s 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 1035s 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 1035s 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 1035s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (1) 1035s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1035s 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 1035s 50 reads; of these: 1035s 50 (100.00%) were unpaired; of these: 1035s 43 (86.00%) aligned 0 times 1035s 2 (4.00%) aligned exactly 1 time 1035s 5 (10.00%) aligned >1 times 1035s 14.00% overall alignment rate 1035s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1035s Flattened IUPAC characters 1035s Mutating sequence Sim.pm.1 1035s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1035s Finished SNPs 1035s Finished ref gaps 1035s Finished read gaps 1035s Mutating sequence Sim.pm.2 1035s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1035s Finished SNPs 1035s Finished ref gaps 1035s Finished read gaps 1035s Mutated reference genome to subject genome 1035s SNPs introduced: 8 1035s Reference gaps introduced: 1 1035s Read gaps introduced: 0 1035s Rearrangements introduced: 0 1035s Created read sampler 1035s Sampling 88 reads 1035s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1035s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1035s parsing sequence Sim.pm.1... 1035s parsing sequence Sim.pm.2... 1035s Parsed 81 reference bases 1035s *** Run 67 of 100 1035s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 4 -k 2 --large-index --mp 6.69445425087056,2.99546601232822 --trim3 4 --rdg 8.32326342280833 --np 6 --score-min L,4.42159737732065,4.40504140799331 --rfg 49.9304515943343 -i S -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1036s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1036s Warning: skipping read '5' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1036s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1036s Warning: skipping mate #2 of read '6' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1036s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1036s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 1036s Warning: skipping mate #2 of read '10' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1036s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1036s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1036s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1036s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1036s Warning: skipping read '26' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1036s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1036s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '49' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1036s Read 50 alignments... 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1036s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '78' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1036s Read 100 alignments... 1036s 88 reads; of these: 1036s 74 (84.09%) were paired; of these: 1036s 73 (98.65%) aligned concordantly 0 times 1036s 0 (0.00%) aligned concordantly exactly 1 time 1036s 1 (1.35%) aligned concordantly >1 times 1036s ---- 1036s 73 pairs aligned concordantly 0 times; of these: 1036s 0 (0.00%) aligned discordantly 1 time 1036s ---- 1036s 73 pairs aligned 0 times concordantly or discordantly; of these: 1036s 146 mates make up the pairs; of these: 1036s 129 (88.36%) aligned 0 times 1036s 6 (4.11%) aligned exactly 1 time 1036s 11 (7.53%) aligned >1 times 1036s 14 (15.91%) were unpaired; of these: 1036s 13 (92.86%) aligned 0 times 1036s 1 (7.14%) aligned exactly 1 time 1036s 0 (0.00%) aligned >1 times 1036s 12.35% overall alignment rate 1036s Read 150 alignments... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s CGA 1036s CGA 1036s Processing line... 1036s CGA 1036s CGA 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s CAACCGAAAGACGGAC 1036s CAACCGAAAGACGGAC 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s CGTATCGCGTAG 1036s CGTATCGCGTAG 1036s Processing line... 1036s CGTATCGCGTAG 1036s CGTATCGCGTAG 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s TGACAACC 1036s TGACAACC 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s GTATCGCG 1036s GTATCGCG 1036s Processing line... 1036s GTATCGCG 1036s GTATCGCG 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s AAGACGGACG 1036s AAGACGGACG 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s ATCGCGT 1036s ATCGCGT 1036s Processing line... 1036s ATCGCGT 1036s ATCGCGT 1036s Processing line... 1036s Processing line... 1036s TC 1036s TC 1036s Processing line... 1036s CCCGTATCGCGTA 1036s CCCGTATCGCGTA 1036s Processing line... 1036s TC 1036s TC 1036s Processing line... 1036s CCCGTATCGCGTA 1036s CCCGTATCGCGTA 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s AAA 1036s AAA 1036s Processing line... 1036s Processing line... 1036s GTATC 1036s GTATC 1036s Processing line... 1036s GTATC 1036s GTATC 1036s Processing line... 1036s Processing line... 1036s AGACG 1036s AGACG 1036s Processing line... 1036s Processing line... 1036s ATCCCGTATCG 1036s ATCCCGTATCG 1036s Processing line... 1036s ATCCCGTATCG 1036s ATCCCGTATCG 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s AACCGAAAG 1036s AACCGAAAG 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s GTG 1036s GTG 1036s Processing line... 1036s CAC 1036s CAC 1036s Processing line... 1036s Processing line... 1036s ACG 1036s ACG 1036s Processing line... 1036s ACG 1036s ACG 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s ACG 1036s ACG 1036s Processing line... 1036s ACG 1036s ACG 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s CCCGTAT 1036s CCCGTAT 1036s Processing line... 1036s CCCGTAT 1036s CCCGTAT 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s AA 1036s AA 1036s Processing line... 1036s AA 1036s AA 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s AAAGA 1036s AAAGA 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s Processing line... 1036s --- Summary --- 1036s Read 1 reference strings 1036s Checked 33 alignments, 0 edits 1036s --------------- 1036s PASSED 1036s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 4 -k 2 --large-index --mp 6.69445425087056,2.99546601232822 --trim3 4 --rdg 8.32326342280833 --np 6 --score-min L,4.42159737732065,4.40504140799331 --rfg 49.9304515943343 -i S -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1036s ALSO checking that bowtie2 and bowtie2-align match up 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1036s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1036s Warning: skipping read '5' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1036s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1036s Warning: skipping mate #2 of read '6' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1036s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1036s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 1036s Warning: skipping mate #2 of read '10' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1036s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1036s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1036s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1036s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1036s Warning: skipping read '26' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1036s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1036s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '49' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1036s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '78' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1036s 88 reads; of these: 1036s 74 (84.09%) were paired; of these: 1036s 73 (98.65%) aligned concordantly 0 times 1036s 0 (0.00%) aligned concordantly exactly 1 time 1036s 1 (1.35%) aligned concordantly >1 times 1036s ---- 1036s 73 pairs aligned concordantly 0 times; of these: 1036s 0 (0.00%) aligned discordantly 1 time 1036s ---- 1036s 73 pairs aligned 0 times concordantly or discordantly; of these: 1036s 146 mates make up the pairs; of these: 1036s 129 (88.36%) aligned 0 times 1036s 6 (4.11%) aligned exactly 1 time 1036s 11 (7.53%) aligned >1 times 1036s 14 (15.91%) were unpaired; of these: 1036s 13 (92.86%) aligned 0 times 1036s 1 (7.14%) aligned exactly 1 time 1036s 0 (0.00%) aligned >1 times 1036s 12.35% overall alignment rate 1036s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1036s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 4 -k 2 --large-index --mp 6.69445425087056,2.99546601232822 --trim3 4 --rdg 8.32326342280833 --np 6 --score-min L,4.42159737732065,4.40504140799331 --rfg 49.9304515943343 -i S -q -p 3 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1036s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1036s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1036s Warning: skipping read '5' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1036s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1036s Warning: skipping mate #2 of read '6' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1036s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1036s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 1036s Warning: skipping mate #2 of read '10' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1036s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1036s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1036s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '49' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1036s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1036s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1036s Warning: skipping read '26' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1036s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1036s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 1036s Warning: skipping mate #1 of read '78' because it was < 2 characters long 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1036s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1036s 88 reads; of these: 1036s 74 (84.09%) were paired; of these: 1036s 73 (98.65%) aligned concordantly 0 times 1036s 0 (0.00%) aligned concordantly exactly 1 time 1036s 1 (1.35%) aligned concordantly >1 times 1036s ---- 1036s 73 pairs aligned concordantly 0 times; of these: 1036s 0 (0.00%) aligned discordantly 1 time 1036s ---- 1036s 73 pairs aligned 0 times concordantly or discordantly; of these: 1036s 146 mates make up the pairs; of these: 1036s 129 (88.36%) aligned 0 times 1036s 6 (4.11%) aligned exactly 1 time 1036s 11 (7.53%) aligned >1 times 1036s 14 (15.91%) were unpaired; of these: 1036s 13 (92.86%) aligned 0 times 1036s 1 (7.14%) aligned exactly 1 time 1036s 0 (0.00%) aligned >1 times 1036s 12.35% overall alignment rate 1036s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1036s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1036s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1036s Flattened IUPAC characters 1036s Mutating sequence Sim.pm.2 1036s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1036s Finished SNPs 1036s Finished ref gaps 1036s Finished read gaps 1036s Mutating sequence Sim.pm.1 1036s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1036s Finished SNPs 1036s Finished ref gaps 1036s Finished read gaps 1036s Mutated reference genome to subject genome 1036s SNPs introduced: 2 1036s Reference gaps introduced: 1 1036s Read gaps introduced: 0 1036s Rearrangements introduced: 0 1036s Created read sampler 1036s Sampling 58 reads 1036s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1036s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1036s parsing sequence Sim.pm.1... 1036s parsing sequence Sim.pm.2... 1036s Parsed 81 reference bases 1036s *** Run 68 of 100 1036s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 2 --large-index -k 3 --rdg 3.61253162802439 --mp 9.59833240735263,7.87540963683735 --local --norc --np 1 --score-min L,8.12387202611618,8.1068132766891 --rfg 43.3122042671486,12.1600499300306 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1037s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 1037s Warning: skipping mate #2 of read '9' because it was < 2 characters long 1037s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 1037s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1037s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 1037s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1037s Read 50 alignments... 1037s 58 reads; of these: 1037s 58 (100.00%) were paired; of these: 1037s 58 (100.00%) aligned concordantly 0 times 1037s 0 (0.00%) aligned concordantly exactly 1 time 1037s 0 (0.00%) aligned concordantly >1 times 1037s ---- 1037s 58 pairs aligned concordantly 0 times; of these: 1037s 0 (0.00%) aligned discordantly 1 time 1037s ---- 1037s 58 pairs aligned 0 times concordantly or discordantly; of these: 1037s 116 mates make up the pairs; of these: 1037s 116 (100.00%) aligned 0 times 1037s 0 (0.00%) aligned exactly 1 time 1037s 0 (0.00%) aligned >1 times 1037s 0.00% overall alignment rate 1037s Read 100 alignments... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s --- Summary --- 1037s Read 1 reference strings 1037s Checked 0 alignments, 0 edits 1037s --------------- 1037s PASSED 1037s Flattened IUPAC characters 1037s Mutating sequence Sim.pm.1 1037s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1037s Finished SNPs 1037s Finished ref gaps 1037s Finished read gaps 1037s Mutating sequence Sim.pm.2 1037s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1037s Finished SNPs 1037s Finished ref gaps 1037s Finished read gaps 1037s Mutated reference genome to subject genome 1037s SNPs introduced: 5 1037s Reference gaps introduced: 0 1037s Read gaps introduced: 0 1037s Rearrangements introduced: 0 1037s Created read sampler 1037s Sampling 110 reads 1037s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1037s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1037s parsing sequence Sim.pm.1... 1037s parsing sequence Sim.pm.2... 1037s Parsed 81 reference bases 1037s *** Run 69 of 100 1037s /usr/bin/bowtie2 --cp-ival 5 --mm --cp-min 2 --score-min L,5.29409119579836,6.73127063045185 --large-index --n-ceil 1.36946824165285,0.248006170653051 -a --mp 8.55639372407155,2.1984271620709 --trim3 8 -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1037s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '2' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1037s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '5' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1037s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '8' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1037s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '10' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1037s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '13' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1037s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '21' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1037s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '22' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1037s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '27' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1037s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '38' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1037s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '43' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1037s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '47' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1037s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '49' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1037s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '53' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1037s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '56' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1037s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '59' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1037s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '61' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1037s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '66' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1037s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '67' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1037s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '69' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1037s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '73' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1037s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '78' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1037s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '86' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1037s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '88' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1037s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '89' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1037s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '93' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1037s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '95' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1037s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '96' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1037s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '98' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1037s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '99' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1037s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '103' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1037s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '104' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1037s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '108' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1037s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '109' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1037s 110 reads; of these: 1037s 110 (100.00%) were unpaired; of these: 1037s 97 (88.18%) aligned 0 times 1037s 9 (8.18%) aligned exactly 1 time 1037s 4 (3.64%) aligned >1 times 1037s 11.82% overall alignment rate 1037s Read 50 alignments... 1037s Read 100 alignments... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s ATC 1037s ATC 1037s Processing line... 1037s ATC 1037s ATC 1037s Processing line... 1037s ATC 1037s ATC 1037s Processing line... 1037s ATC 1037s ATC 1037s Processing line... 1037s GAT 1037s GAT 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s ACCGAAAGACGGA 1037s ACCGAAAGACGGA 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s AGA 1037s AGA 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s TGTTCACGTGGGCGAC 1037s TGTTCACGTGGGCGAC 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s GATGACA 1037s GATGACA 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s GT 1037s GT 1037s Processing line... 1037s AC 1037s AC 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s GATGACAACCGAA 1037s GATGACAACCGAA 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s TGACAACCG 1037s TGACAACCG 1037s Processing line... 1037s Processing line... 1037s GTGGGCGA 1037s GTGGGCGA 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s GGACGTA 1037s GGACGTA 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s AGA 1037s AGA 1037s Processing line... 1037s Processing line... 1037s Processing line... 1037s ATCC 1037s ATCC 1037s Processing line... 1037s ATCC 1037s ATCC 1037s --- Summary --- 1037s Read 1 reference strings 1037s /usr/bin/bowtie2 --cp-ival 5 --mm --cp-min 2 --score-min L,5.29409119579836,6.73127063045185 --large-index --n-ceil 1.36946824165285,0.248006170653051 -a --mp 8.55639372407155,2.1984271620709 --trim3 8 -f -p 2 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1037s Checked 42 alignments, 0 edits 1037s --------------- 1037s PASSED 1037s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1037s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '2' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1037s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '5' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1037s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '8' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1037s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '10' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1037s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '13' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1037s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '21' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1037s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '22' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1037s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '27' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1037s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '38' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1037s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '43' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1037s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '47' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1037s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '49' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1037s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '53' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1037s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '56' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1037s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '59' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1037s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '66' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1037s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '67' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1037s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '69' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1037s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '73' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1037s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '78' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1037s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '61' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1037s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '98' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1037s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '99' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1037s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '103' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1037s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '104' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1037s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '108' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1037s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '109' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1037s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '86' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1037s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '88' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1037s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 1037s Warning: skipping read '89' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1037s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '93' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1037s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '95' because it was < 2 characters long 1037s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1037s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1037s Warning: skipping read '96' because it was < 2 characters long 1037s 110 reads; of these: 1037s 110 (100.00%) were unpaired; of these: 1037s 97 (88.18%) aligned 0 times 1037s 9 (8.18%) aligned exactly 1 time 1037s 4 (3.64%) aligned >1 times 1037s 11.82% overall alignment rate 1037s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1037s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1037s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1037s Flattened IUPAC characters 1037s Mutating sequence Sim.pm.1 1037s Introducing 12 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1037s Finished SNPs 1037s Finished ref gaps 1037s Finished read gaps 1037s Mutating sequence Sim.pm.2 1037s Introducing 3 SNPs, 1/0 ref/read gaps, and 3 rearrangements 1037s Finished SNPs 1037s Finished ref gaps 1037s Finished read gaps 1037s Mutated reference genome to subject genome 1037s SNPs introduced: 15 1037s Reference gaps introduced: 1 1037s Read gaps introduced: 1 1037s Rearrangements introduced: 3 1037s Created read sampler 1037s Sampling 120 reads 1037s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1037s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1037s parsing sequence Sim.pm.1... 1037s parsing sequence Sim.pm.2... 1037s Parsed 81 reference bases 1037s *** Run 70 of 100 1037s /usr/bin/bowtie2 -R 3 --rfg 45.0507364102232,11.158325421837 --score-min L,3.97679215065545,2.22298803783673 --n-ceil 0.937388318906542,0.957006391764406 --cp-min 6 --cp-ival 2 --mm --local --trim3 5 --large-index -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1038s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '14' because it was < 2 characters long 1038s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '18' because it was < 2 characters long 1038s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '22' because it was < 2 characters long 1038s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '25' because it was < 2 characters long 1038s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '32' because it was < 2 characters long 1038s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '37' because it was < 2 characters long 1038s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '41' because it was < 2 characters long 1038s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '44' because it was < 2 characters long 1038s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '64' because it was < 2 characters long 1038s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '68' because it was < 2 characters long 1038s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '73' because it was < 2 characters long 1038s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '77' because it was < 2 characters long 1038s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 1038s Warning: skipping read '82' because it was < 2 characters long 1038s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 1038s Warning: skipping read '89' because it was < 2 characters long 1038s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '92' because it was < 2 characters long 1038s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '94' because it was < 2 characters long 1038s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '102' because it was < 2 characters long 1038s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '105' because it was < 2 characters long 1038s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '109' because it was < 2 characters long 1038s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '113' because it was < 2 characters long 1038s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '115' because it was < 2 characters long 1038s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '116' because it was < 2 characters long 1038s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '118' because it was < 2 characters long 1038s 120 reads; of these: 1038s 120 (100.00%) were unpaired; of these: 1038s 120 (100.00%) aligned 0 times 1038s 0 (0.00%) aligned exactly 1 time 1038s 0 (0.00%) aligned >1 times 1038s 0.00% overall alignment rate 1038s Read 50 alignments... 1038s Read 100 alignments... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s --- Summary --- 1038s Read 1 reference strings 1038s Checked 0 alignments, 0 edits 1038s --------------- 1038s PASSED 1038s Flattened IUPAC characters 1038s Mutating sequence Sim.pm.2 1038s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1038s Finished SNPs 1038s Finished ref gaps 1038s Finished read gaps 1038s Mutating sequence Sim.pm.1 1038s Introducing 3 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1038s Finished SNPs 1038s Finished ref gaps 1038s Finished read gaps 1038s Mutated reference genome to subject genome 1038s SNPs introduced: 6 1038s Reference gaps introduced: 0 1038s Read gaps introduced: 1 1038s Rearrangements introduced: 2 1038s Created read sampler 1038s Sampling 80 reads 1038s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1038s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1038s parsing sequence Sim.pm.1... 1038s *** Run 71 of 100 1038s /usr/bin/bowtie2 --large-index --ma 9.55388502128433 --rdg 46.1975415757816,3.32712600045172 --mp 6.77973459953323,4.69885563682892 --cp-ival 1 --cp-min 9 --score-min L,9.97824704095302,3.01676437464774 --rfg 4.52943440387115 -N 1 -L12 --norc -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1038s parsing sequence Sim.pm.2... 1038s Parsed 81 reference bases 1038s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1038s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (1) 1038s Warning: skipping mate #2 of read '15' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1038s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (1) 1038s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1038s Warning: skipping mate #1 of read '33' because length (1) <= # seed mismatches (1) 1038s Warning: skipping mate #1 of read '33' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1038s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (1) 1038s Warning: skipping mate #2 of read '76' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1038s Read 50 alignments... 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1038s Read 100 alignments... 1038s 80 reads; of these: 1038s 80 (100.00%) were paired; of these: 1038s 79 (98.75%) aligned concordantly 0 times 1038s 1 (1.25%) aligned concordantly exactly 1 time 1038s 0 (0.00%) aligned concordantly >1 times 1038s ---- 1038s 79 pairs aligned concordantly 0 times; of these: 1038s 0 (0.00%) aligned discordantly 1 time 1038s ---- 1038s 79 pairs aligned 0 times concordantly or discordantly; of these: 1038s 158 mates make up the pairs; of these: 1038s 140 (88.61%) aligned 0 times 1038s 5 (3.16%) aligned exactly 1 time 1038s 13 (8.23%) aligned >1 times 1038s 12.50% overall alignment rate 1038s Read 150 alignments... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s TCCCGTATCG 1038s TCCCGTATCG 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s CCCGTATCGCGTAG 1038s CCCGTATCGCGTAG 1038s Processing line... 1038s Processing line... 1038s CGG 1038s CGG 1038s Processing line... 1038s Processing line... 1038s CGCG 1038s CGCG 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s AGACGGA 1038s AGACGGA 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s TG 1038s TG 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s CCGAAAGACGGACG 1038s CCGAAAGACGGACG 1038s Processing line... 1038s AAAGACGGACGTA 1038s AAAGACGGACGTA 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s TCCC 1038s TCCC 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s CGGACGT 1038s CGGACGT 1038s Processing line... 1038s GA 1038s GA 1038s Processing line... 1038s CCCGT 1038s CCCGT 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s AGACGGACGTA 1038s AGACGGACGTA 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s TCGCG 1038s TCGCG 1038s Processing line... 1038s Processing line... 1038s TCC 1038s TCC 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s CG 1038s CG 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s TCCCGTATCGC 1038s TCCCGTATCGC 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s CCC 1038s CCC 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s GT 1038s GT 1038s Processing line... 1038s Processing line... 1038s CCGAAAGACG 1038s CCGAAAGACG 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s --- Summary --- 1038s Read 1 reference strings 1038s Checked 20 alignments, 0 edits 1038s --------------- 1038s PASSED 1038s Flattened IUPAC characters 1038s Mutating sequence Sim.pm.1 1038s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1038s Finished SNPs 1038s Finished ref gaps 1038s Finished read gaps 1038s Mutating sequence Sim.pm.2 1038s Introducing 7 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1038s Finished SNPs 1038s Finished ref gaps 1038s Finished read gaps 1038s Mutated reference genome to subject genome 1038s SNPs introduced: 17 1038s Reference gaps introduced: 1 1038s Read gaps introduced: 1 1038s Rearrangements introduced: 1 1038s Created read sampler 1038s Sampling 102 reads 1038s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1038s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1038s parsing sequence Sim.pm.1... 1038s parsing sequence Sim.pm.2... 1038s Parsed 81 reference bases 1038s *** Run 72 of 100 1038s /usr/bin/bowtie2 --cp-min 2 --mm --cp-ival 2 --rdg 10.240425400639 -a --large-index --norc --trim5 8 --rfg 8.76460225972868,9.47269020563861 --score-min L,7.21996839470105,5.76360303019465 -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1038s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '15' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1038s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '18' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1038s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '21' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1038s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '24' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1038s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '25' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1038s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '30' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1038s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '36' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1038s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '38' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1038s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '42' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1038s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '43' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1038s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '46' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1038s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '54' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1038s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '55' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1038s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '58' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1038s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '61' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1038s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '63' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1038s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '70' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1038s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '72' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1038s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '83' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1038s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '84' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1038s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '88' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1038s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '89' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1038s Warning: skipping read '90' because length (1) <= # seed mismatches (0) 1038s Warning: skipping read '90' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1038s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '94' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1038s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '99' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1038s 102 reads; of these: 1038s 102 (100.00%) were unpaired; of these: 1038s 97 (95.10%) aligned 0 times 1038s 2 (1.96%) aligned exactly 1 time 1038s 3 (2.94%) aligned >1 times 1038s 4.90% overall alignment rate 1038s Read 50 alignments... 1038s Read 100 alignments... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s GGACGTA 1038s GGACGTA 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s CT 1038s CT 1038s Processing line... 1038s CT 1038s CT 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s GA 1038s GA 1038s Processing line... 1038s GA 1038s GA 1038s Processing line... 1038s GA 1038s GA 1038s Processing line... 1038s GA 1038s GA 1038s Processing line... 1038s GA 1038s GA 1038s Processing line... 1038s GA 1038s GA 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s GAC 1038s GAC 1038s Processing line... 1038s GAC 1038s GAC 1038s Processing line... 1038s GAC 1038s GAC 1038s Processing line... 1038s GAC 1038s GAC 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s /usr/bin/bowtie2 --cp-min 2 --mm --cp-ival 2 --rdg 10.240425400639 -a --large-index --norc --trim5 8 --rfg 8.76460225972868,9.47269020563861 --score-min L,7.21996839470105,5.76360303019465 -f -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s ACA 1038s ACA 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s Processing line... 1038s --- Summary --- 1038s Read 1 reference strings 1038s Checked 14 alignments, 0 edits 1038s --------------- 1038s PASSED 1038s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1038s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '15' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1038s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '18' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1038s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '21' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1038s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '24' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1038s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '25' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1038s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '36' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1038s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '38' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1038s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '42' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1038s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '43' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1038s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '46' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1038s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '30' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1038s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '54' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1038s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '55' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1038s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '58' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1038s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '61' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1038s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '63' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1038s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '83' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1038s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '84' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1038s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '88' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1038s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '89' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1038s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '70' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1038s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '72' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1038s Warning: skipping read '90' because length (1) <= # seed mismatches (0) 1038s Warning: skipping read '90' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1038s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '94' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1038s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1038s Warning: skipping read '99' because it was < 2 characters long 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1038s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1038s 102 reads; of these: 1038s 102 (100.00%) were unpaired; of these: 1038s 97 (95.10%) aligned 0 times 1038s 2 (1.96%) aligned exactly 1 time 1038s 3 (2.94%) aligned >1 times 1038s 4.90% overall alignment rate 1038s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1039s Flattened IUPAC characters 1039s Mutating sequence Sim.pm.2 1039s Introducing 0 SNPs, 1/2 ref/read gaps, and 0 rearrangements 1039s Finished SNPs 1039s Finished ref gaps 1039s Finished read gaps 1039s Mutating sequence Sim.pm.1 1039s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1039s Finished SNPs 1039s Finished ref gaps 1039s Finished read gaps 1039s Mutated reference genome to subject genome 1039s SNPs introduced: 1 1039s Reference gaps introduced: 1 1039s Read gaps introduced: 3 1039s Rearrangements introduced: 0 1039s Created read sampler 1039s Sampling 126 reads 1039s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1039s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1039s parsing sequence Sim.pm.1... 1039s parsing sequence Sim.pm.2... 1039s Parsed 81 reference bases 1039s *** Run 73 of 100 1039s /usr/bin/bowtie2 --mm --cp-ival 2 --cp-min 2 --norc --n-ceil 0.534645409064768,0.942614022932105 --large-index -M 4 --score-min L,6.02057792979717,7.40394024659643 --rdg 14.9242861199027,3.58301197856479 --mp 7.65016080358237,2.51533618373963 --rfg 18.6923403254938,7.42049904341922 -f -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta 1039s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1039s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #2 of read '3' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1039s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #2 of read '39' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1039s Warning: skipping mate #1 of read '69' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1039s Warning: skipping mate #1 of read '71' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1039s Read 50 alignments... 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1039s Read 100 alignments... 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1039s Warning: skipping mate #1 of read '90' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read '90' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1039s Warning: skipping mate #2 of read '96' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #2 of read '96' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1039s Warning: skipping mate #1 of read '109' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read '109' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1039s Warning: skipping mate #2 of read '113' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #2 of read '113' because it was < 2 characters long 1039s Read 150 alignments... 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 1039s Warning: skipping mate #1 of read '124' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read '124' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 1039s Read 200 alignments... 1039s 126 reads; of these: 1039s 126 (100.00%) were paired; of these: 1039s 125 (99.21%) aligned concordantly 0 times 1039s 0 (0.00%) aligned concordantly exactly 1 time 1039s 1 (0.79%) aligned concordantly >1 times 1039s ---- 1039s 125 pairs aligned concordantly 0 times; of these: 1039s 0 (0.00%) aligned discordantly 1 time 1039s ---- 1039s 125 pairs aligned 0 times concordantly or discordantly; of these: 1039s 250 mates make up the pairs; of these: 1039s 226 (90.40%) aligned 0 times 1039s 8 (3.20%) aligned exactly 1 time 1039s 16 (6.40%) aligned >1 times 1039s 10.32% overall alignment rate 1039s Read 250 alignments... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s GATGACAACCGAAAG 1039s GATGACAACCGAAAG 1039s Processing line... 1039s Processing line... 1039s TATC 1039s TATC 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s ACAACCGA 1039s ACAACCGA 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s CG 1039s CG 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s AAAGA 1039s AAAGA 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s AAA 1039s AAA 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s GC 1039s GC 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s CGC 1039s CGC 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s TC 1039s TC 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s GG 1039s GG 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s TATCGCG 1039s TATCGCG 1039s Processing line... 1039s ACCG 1039s ACCG 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s AC 1039s AC 1039s Processing line... 1039s Processing line... 1039s CGA 1039s CGA 1039s Processing line... 1039s Processing line... 1039s TC 1039s TC 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s CCGAAAGAC 1039s CCGAAAGAC 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s AC 1039s AC 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s AA 1039s AA 1039s Processing line... 1039s Processing line... 1039s CC 1039s CC 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s AC 1039s AC 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s GT 1039s GT 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s TCGC 1039s TCGC 1039s Processing line... 1039s Processing line... 1039s CCGAAAGACGGAC 1039s CCGAAAGACGGAC 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s CCG 1039s CCG 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s CCGAAAGACG 1039s CCGAAAGACG 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s CAACCGAAAGACG 1039s CAACCGAAAGACG 1039s Processing line... 1039s Processing line... 1039s Processing line... 1039s --- Summary --- 1039s Read 1 reference strings 1039s Checked 26 alignments, 0 edits 1039s --------------- 1039s PASSED 1039s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1039s /usr/bin/bowtie2 --mm --cp-ival 2 --cp-min 2 --norc --n-ceil 0.534645409064768,0.942614022932105 --large-index -M 4 --score-min L,6.02057792979717,7.40394024659643 --rdg 14.9242861199027,3.58301197856479 --mp 7.65016080358237,2.51533618373963 --rfg 18.6923403254938,7.42049904341922 -f -p 4 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1039s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1039s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #2 of read '3' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1039s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #2 of read '39' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1039s Warning: skipping mate #1 of read '69' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1039s Warning: skipping mate #1 of read '71' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1039s Warning: skipping mate #2 of read '113' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #2 of read '113' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1039s Warning: skipping mate #1 of read '90' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read '90' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1039s Warning: skipping mate #2 of read '96' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #2 of read '96' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 1039s Warning: skipping mate #1 of read '124' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read '124' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1039s Warning: skipping mate #1 of read '109' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read '109' because it was < 2 characters long 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1039s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1039s 126 reads; of these: 1039s 126 (100.00%) were paired; of these: 1039s 125 (99.21%) aligned concordantly 0 times 1039s 0 (0.00%) aligned concordantly exactly 1 time 1039s 1 (0.79%) aligned concordantly >1 times 1039s ---- 1039s 125 pairs aligned concordantly 0 times; of these: 1039s 0 (0.00%) aligned discordantly 1 time 1039s ---- 1039s 125 pairs aligned 0 times concordantly or discordantly; of these: 1039s 250 mates make up the pairs; of these: 1039s 226 (90.40%) aligned 0 times 1039s 8 (3.20%) aligned exactly 1 time 1039s 16 (6.40%) aligned >1 times 1039s 10.32% overall alignment rate 1039s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1039s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1039s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1039s Flattened IUPAC characters 1039s Mutating sequence Sim.pm.1 1039s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1039s Finished SNPs 1039s Finished ref gaps 1039s Finished read gaps 1039s Mutating sequence Sim.pm.2 1039s Introducing 13 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1039s Finished SNPs 1039s Finished ref gaps 1039s Finished read gaps 1039s Mutated reference genome to subject genome 1039s SNPs introduced: 13 1039s Reference gaps introduced: 1 1039s Read gaps introduced: 1 1039s Rearrangements introduced: 0 1039s Created read sampler 1039s Sampling 155 reads 1039s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1039s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1039s parsing sequence Sim.pm.1... 1039s *** Run 74 of 100 1039s /usr/bin/bowtie2 -k 9 --large-index --local --trim3 2 --rdg 19.2614558489173 --cp-ival 1 --mm --cp-min 3 --score-min L,8.6676894057326,5.93908649488462 --gbar 1 --trim5 7 -D 40 --np 7 --nofw --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq 1039s parsing sequence Sim.pm.2... 1039s Parsed 81 reference bases 1039s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1039s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1039s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1039s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 1039s Read 50 alignments... 1039s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 1039s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 1039s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (1) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 1040s Read 100 alignments... 1040s Read 150 alignments... 1040s 155 reads; of these: 1040s 119 (76.77%) were paired; of these: 1040s 119 (100.00%) aligned concordantly 0 times 1040s 0 (0.00%) aligned concordantly exactly 1 time 1040s 0 (0.00%) aligned concordantly >1 times 1040s ---- 1040s 119 pairs aligned concordantly 0 times; of these: 1040s 0 (0.00%) aligned discordantly 1 time 1040s ---- 1040s 119 pairs aligned 0 times concordantly or discordantly; of these: 1040s 238 mates make up the pairs; of these: 1040s 238 (100.00%) aligned 0 times 1040s 0 (0.00%) aligned exactly 1 time 1040s 0 (0.00%) aligned >1 times 1040s 36 (23.23%) were unpaired; of these: 1040s 36 (100.00%) aligned 0 times 1040s 0 (0.00%) aligned exactly 1 time 1040s 0 (0.00%) aligned >1 times 1040s 0.00% overall alignment rate 1040s Read 200 alignments... 1040s Read 250 alignments... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing 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line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s /usr/bin/bowtie2 -k 9 --large-index --local --trim3 2 --rdg 19.2614558489173 --cp-ival 1 --mm --cp-min 3 --score-min L,8.6676894057326,5.93908649488462 --gbar 1 --trim5 7 -D 40 --np 7 --nofw --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s --- Summary --- 1040s Read 1 reference strings 1040s Checked 0 alignments, 0 edits 1040s --------------- 1040s PASSED 1040s ALSO checking that bowtie2 and bowtie2-align match up 1040s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1040s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1040s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1040s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (1) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 1040s 155 reads; of these: 1040s 119 (76.77%) were paired; of these: 1040s 119 (100.00%) aligned concordantly 0 times 1040s 0 (0.00%) aligned concordantly exactly 1 time 1040s 0 (0.00%) aligned concordantly >1 times 1040s ---- 1040s 119 pairs aligned concordantly 0 times; of these: 1040s 0 (0.00%) aligned discordantly 1 time 1040s ---- 1040s 119 pairs aligned 0 times concordantly or discordantly; of these: 1040s 238 mates make up the pairs; of these: 1040s 238 (100.00%) aligned 0 times 1040s 0 (0.00%) aligned exactly 1 time 1040s 0 (0.00%) aligned >1 times 1040s 36 (23.23%) were unpaired; of these: 1040s 36 (100.00%) aligned 0 times 1040s 0 (0.00%) aligned exactly 1 time 1040s 0 (0.00%) aligned >1 times 1040s 0.00% overall alignment rate 1040s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1040s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1040s /usr/bin/bowtie2 -k 9 --large-index --local --trim3 2 --rdg 19.2614558489173 --cp-ival 1 --mm --cp-min 3 --score-min L,8.6676894057326,5.93908649488462 --gbar 1 --trim5 7 -D 40 --np 7 --nofw --qseq -p 3 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1040s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1040s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1040s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1040s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (1) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 1040s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 1040s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 1040s 155 reads; of these: 1040s 119 (76.77%) were paired; of these: 1040s 119 (100.00%) aligned concordantly 0 times 1040s 0 (0.00%) aligned concordantly exactly 1 time 1040s 0 (0.00%) aligned concordantly >1 times 1040s ---- 1040s 119 pairs aligned concordantly 0 times; of these: 1040s 0 (0.00%) aligned discordantly 1 time 1040s ---- 1040s 119 pairs aligned 0 times concordantly or discordantly; of these: 1040s 238 mates make up the pairs; of these: 1040s 238 (100.00%) aligned 0 times 1040s 0 (0.00%) aligned exactly 1 time 1040s 0 (0.00%) aligned >1 times 1040s 36 (23.23%) were unpaired; of these: 1040s 36 (100.00%) aligned 0 times 1040s 0 (0.00%) aligned exactly 1 time 1040s 0 (0.00%) aligned >1 times 1040s 0.00% overall alignment rate 1040s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1040s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1040s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1040s Flattened IUPAC characters 1040s Mutating sequence Sim.pm.1 1040s Introducing 0 SNPs, 0/3 ref/read gaps, and 0 rearrangements 1040s Finished SNPs 1040s Finished ref gaps 1040s Finished read gaps 1040s Mutating sequence Sim.pm.2 1040s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1040s Finished SNPs 1040s Finished ref gaps 1040s Finished read gaps 1040s Mutated reference genome to subject genome 1040s SNPs introduced: 2 1040s Reference gaps introduced: 0 1040s Read gaps introduced: 3 1040s Rearrangements introduced: 1 1040s Created read sampler 1040s Sampling 12 reads 1040s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1040s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1040s parsing sequence Sim.pm.1... 1040s parsing sequence Sim.pm.2... 1040s Parsed 81 reference bases 1040s *** Run 75 of 100 1040s /usr/bin/bowtie2 --cp-min 3 --mm --cp-ival 1 --trim5 1 --mp 9.57786707632183,7.12393212762393 --trim3 1 --rfg 40.9732521035366 --large-index --score-min L,3.2692916895681,5.705915895292 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1040s 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 1040s 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 1040s 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 1040s 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 1040s 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 1040s 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 1040s 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 1040s 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 1040s 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 1040s 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 1040s 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 1040s 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 1040s 12 reads; of these: 1040s 12 (100.00%) were unpaired; of these: 1040s 11 (91.67%) aligned 0 times 1040s 0 (0.00%) aligned exactly 1 time 1040s 1 (8.33%) aligned >1 times 1040s 8.33% overall alignment rate 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s CGCGT 1040s CGCGT 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s Processing line... 1040s --- Summary --- 1040s Read 1 reference strings 1040s Checked 1 alignments, 0 edits 1040s --------------- 1040s PASSED 1040s Flattened IUPAC characters 1040s Mutating sequence Sim.pm.2 1040s Introducing 9 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1040s Finished SNPs 1040s Finished ref gaps 1040s Finished read gaps 1040s Mutating sequence Sim.pm.1 1040s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1040s Finished SNPs 1040s Finished ref gaps 1040s Finished read gaps 1040s Mutated reference genome to subject genome 1040s SNPs introduced: 15 1040s Reference gaps introduced: 1 1040s Read gaps introduced: 2 1040s Rearrangements introduced: 0 1040s Created read sampler 1040s Sampling 60 reads 1040s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1040s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1040s parsing sequence Sim.pm.1... 1040s parsing sequence Sim.pm.2... 1040s *** Run 76 of 100 1040s /usr/bin/bowtie2 --local -a --trim3 5 --rdg 48.9956886780605 --large-index --cp-min 11 --cp-ival 2 --mm --rfg 22.3840522662012,18.8551181506762 --trim5 6 --score-min L,8.87951385777382,2.03781398628568 --nofw --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1040s Parsed 81 reference bases 1041s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1041s 60 reads; of these: 1041s 60 (100.00%) were unpaired; of these: 1041s 60 (100.00%) aligned 0 times 1041s 0 (0.00%) aligned exactly 1 time 1041s 0 (0.00%) aligned >1 times 1041s 0.00% overall alignment rate 1041s Read 50 alignments... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s --- Summary --- 1041s Read 1 reference strings 1041s Checked 0 alignments, 0 edits 1041s --------------- 1041s PASSED 1041s Flattened IUPAC characters 1041s Mutating sequence Sim.pm.1 1041s Introducing 12 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1041s Finished SNPs 1041s Finished ref gaps 1041s Finished read gaps 1041s Mutating sequence Sim.pm.2 1041s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1041s Finished SNPs 1041s Finished ref gaps 1041s Finished read gaps 1041s Mutated reference genome to subject genome 1041s SNPs introduced: 14 1041s Reference gaps introduced: 1 1041s Read gaps introduced: 0 1041s Rearrangements introduced: 1 1041s Created read sampler 1041s Sampling 64 reads 1041s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1041s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1041s parsing sequence Sim.pm.1... 1041s parsing sequence Sim.pm.2... 1041s *** Run 77 of 100 1041s /usr/bin/bowtie2 --large-index -M 5 --mp 5.48354600700616,2.09118680458091 --trim3 1 --cp-ival 1 --cp-min 6 --score-min L,9.63279949025622,7.14310715681133 --rfg 47.1854332656422 --trim5 7 -R 2 --nofw --np 5 -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta 1041s Parsed 81 reference bases 1041s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1041s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '2' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1041s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '7' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1041s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '8' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1041s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '9' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1041s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '10' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1041s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '15' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1041s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '16' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1041s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '17' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1041s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '18' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1041s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '27' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1041s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '28' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1041s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '30' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1041s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '32' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1041s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '34' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1041s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '35' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1041s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '42' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1041s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '46' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1041s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '47' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1041s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '54' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1041s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '61' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1041s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '63' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1041s 64 reads; of these: 1041s 64 (100.00%) were unpaired; of these: 1041s 57 (89.06%) aligned 0 times 1041s 3 (4.69%) aligned exactly 1 time 1041s 4 (6.25%) aligned >1 times 1041s 10.94% overall alignment rate 1041s Read 50 alignments... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s AC 1041s AC 1041s Processing line... 1041s TATCGCGTA 1041s TATCGCGTA 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s GCGA 1041s GCGA 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s GGG 1041s GGG 1041s Processing line... 1041s Processing line... 1041s /usr/bin/bowtie2 --large-index -M 5 --mp 5.48354600700616,2.09118680458091 --trim3 1 --cp-ival 1 --cp-min 6 --score-min L,9.63279949025622,7.14310715681133 --rfg 47.1854332656422 --trim5 7 -R 2 --nofw --np 5 -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s GT 1041s GT 1041s Processing line... 1041s ATC 1041s ATC 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s ACAACCGAAAGACG 1041s ACAACCGAAAGACG 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s --- Summary --- 1041s Read 1 reference strings 1041s Checked 7 alignments, 0 edits 1041s --------------- 1041s PASSED 1041s ALSO checking that bowtie2 and bowtie2-align match up 1041s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1041s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '2' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1041s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '7' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1041s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '8' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1041s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '9' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1041s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '10' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1041s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '15' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1041s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '16' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1041s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '17' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1041s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '18' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1041s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '27' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1041s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '28' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1041s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '30' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1041s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '32' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1041s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '34' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1041s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '35' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1041s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '42' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1041s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '46' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1041s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '47' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1041s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '54' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1041s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '61' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1041s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1041s Warning: skipping read '63' because it was < 2 characters long 1041s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1041s 64 reads; of these: 1041s 64 (100.00%) were unpaired; of these: 1041s 57 (89.06%) aligned 0 times 1041s 3 (4.69%) aligned exactly 1 time 1041s 4 (6.25%) aligned >1 times 1041s 10.94% overall alignment rate 1041s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1041s Flattened IUPAC characters 1041s Mutating sequence Sim.pm.1 1041s Introducing 9 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1041s Finished SNPs 1041s Finished ref gaps 1041s Finished read gaps 1041s Mutating sequence Sim.pm.2 1041s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1041s Finished SNPs 1041s Finished ref gaps 1041s Finished read gaps 1041s Mutated reference genome to subject genome 1041s SNPs introduced: 9 1041s Reference gaps introduced: 1 1041s Read gaps introduced: 0 1041s Rearrangements introduced: 1 1041s Created read sampler 1041s Sampling 78 reads 1041s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1041s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1041s parsing sequence Sim.pm.1... 1041s parsing sequence Sim.pm.2... 1041s Parsed 81 reference bases 1041s *** Run 78 of 100 1041s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mm --rdg 8.04487471134139,11.3326143619009 --local --large-index -k 4 --np 2 --rfg 33.9687715216286 --n-ceil 1.17817739613591,0.382215767162079 --score-min L,3.28081437194218,3.29077572362308 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1041s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1041s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 1041s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1041s 78 reads; of these: 1041s 78 (100.00%) were unpaired; of these: 1041s 78 (100.00%) aligned 0 times 1041s 0 (0.00%) aligned exactly 1 time 1041s 0 (0.00%) aligned >1 times 1041s 0.00% overall alignment rate 1041s Read 50 alignments... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s Processing line... 1041s --- Summary --- 1041s Read 1 reference strings 1041s Checked 0 alignments, 0 edits 1041s --------------- 1041s PASSED 1041s Flattened IUPAC characters 1041s Mutating sequence Sim.pm.1 1041s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1041s Finished SNPs 1041s Finished ref gaps 1041s Finished read gaps 1041s Mutating sequence Sim.pm.2 1041s Introducing 10 SNPs, 2/0 ref/read gaps, and 1 rearrangements 1041s Finished SNPs 1041s Finished ref gaps 1041s Finished read gaps 1041s Mutated reference genome to subject genome 1041s SNPs introduced: 11 1041s Reference gaps introduced: 3 1041s Read gaps introduced: 0 1041s Rearrangements introduced: 1 1041s Created read sampler 1041s Sampling 88 reads 1041s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1041s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1041s parsing sequence Sim.pm.1... 1041s parsing sequence Sim.pm.2... 1041s Parsed 81 reference bases 1041s *** Run 79 of 100 1041s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --ma 26.9707958197769 --large-index -k 14 --trim3 5 --mp 7.34090704562939,2.10953066745312 -N 0 -L24 --nofw --np 1 --score-min L,8.68397561606855,4.587604676814 --gbar 7 --trim5 8 -i C,1.78215924719513 --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq 1042s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Read 50 alignments... 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (1) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 1042s 88 reads; of these: 1042s 73 (82.95%) were paired; of these: 1042s 72 (98.63%) aligned concordantly 0 times 1042s 0 (0.00%) aligned concordantly exactly 1 time 1042s 1 (1.37%) aligned concordantly >1 times 1042s ---- 1042s 72 pairs aligned concordantly 0 times; of these: 1042s 0 (0.00%) aligned discordantly 1 time 1042s ---- 1042s 72 pairs aligned 0 times concordantly or discordantly; of these: 1042s 144 mates make up the pairs; of these: 1042s 135 (93.75%) aligned 0 times 1042s 2 (1.39%) aligned exactly 1 time 1042s 7 (4.86%) aligned >1 times 1042s 15 (17.05%) were unpaired; of these: 1042s 14 (93.33%) aligned 0 times 1042s 0 (0.00%) aligned exactly 1 time 1042s 1 (6.67%) aligned >1 times 1042s 7.45% overall alignment rate 1042s Read 100 alignments... 1042s Read 150 alignments... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s ACGTA 1042s ACGTA 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s GCGT 1042s GCGT 1042s Processing line... 1042s GCGT 1042s GCGT 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s ACGGACG 1042s ACGGACG 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s TA 1042s TA 1042s Processing line... 1042s TA 1042s TA 1042s Processing line... 1042s TA 1042s TA 1042s Processing line... 1042s TA 1042s TA 1042s Processing line... 1042s TA 1042s TA 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s AT 1042s AT 1042s Processing line... 1042s AT 1042s AT 1042s Processing line... 1042s AT 1042s AT 1042s Processing line... 1042s AT 1042s AT 1042s Processing line... 1042s AT 1042s AT 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s GC 1042s GC 1042s Processing line... 1042s GC 1042s GC 1042s Processing line... 1042s GC 1042s GC 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s CG 1042s CG 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s AA 1042s AA 1042s Processing line... 1042s AA 1042s AA 1042s Processing line... 1042s AA 1042s AA 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s ATCG 1042s ATCG 1042s Processing line... 1042s ATCG 1042s ATCG 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s AT 1042s AT 1042s Processing line... 1042s GC 1042s GC 1042s Processing line... 1042s AT 1042s AT 1042s Processing line... 1042s GC 1042s GC 1042s Processing line... 1042s AT 1042s AT 1042s Processing line... 1042s GC 1042s GC 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s GG 1042s GG 1042s Processing line... 1042s GG 1042s GG 1042s Processing line... 1042s GG 1042s GG 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s Processing line... 1042s --- Summary --- 1042s Read 1 reference strings 1042s Checked 43 alignments, 0 edits 1042s --------------- 1042s PASSED 1042s ALSO checking that bowtie2 and bowtie2-align match up 1042s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --ma 26.9707958197769 --large-index -k 14 --trim3 5 --mp 7.34090704562939,2.10953066745312 -N 0 -L24 --nofw --np 1 --score-min L,8.68397561606855,4.587604676814 --gbar 7 --trim5 8 -i C,1.78215924719513 --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1042s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 1042s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1042s 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 1043s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1043s 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 1043s 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 1043s 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 1043s 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 1043s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 1043s 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 1043s 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 1043s 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 1043s 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 1043s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1043s 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 1043s 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 1043s 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 1043s 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 1043s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1043s 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 1043s 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 1043s 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 1043s 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 1043s 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 1043s 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 1043s 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 1043s 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 1043s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1043s 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 1043s 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 1043s 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 1043s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1043s 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 1043s 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 1043s 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 1043s 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 1043s 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 1043s 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 1043s 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 1043s 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 1043s 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 1043s 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 1043s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 1043s 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 1043s 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 1043s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 1043s 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 1043s 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 1043s 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 1043s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 1043s 88 reads; of these: 1043s 73 (82.95%) were paired; of these: 1043s 72 (98.63%) aligned concordantly 0 times 1043s 0 (0.00%) aligned concordantly exactly 1 time 1043s 1 (1.37%) aligned concordantly >1 times 1043s ---- 1043s 72 pairs aligned concordantly 0 times; of these: 1043s 0 (0.00%) aligned discordantly 1 time 1043s ---- 1043s 72 pairs aligned 0 times concordantly or discordantly; of these: 1043s 144 mates make up the pairs; of these: 1043s 135 (93.75%) aligned 0 times 1043s 2 (1.39%) aligned exactly 1 time 1043s 7 (4.86%) aligned >1 times 1043s 15 (17.05%) were unpaired; of these: 1043s 14 (93.33%) aligned 0 times 1043s 0 (0.00%) aligned exactly 1 time 1043s 1 (6.67%) aligned >1 times 1043s 7.45% overall alignment rate 1043s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1043s Flattened IUPAC characters 1043s Mutating sequence Sim.pm.2 1043s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1043s Finished SNPs 1043s Finished ref gaps 1043s Finished read gaps 1043s Mutating sequence Sim.pm.1 1043s Introducing 4 SNPs, 3/1 ref/read gaps, and 1 rearrangements 1043s Finished SNPs 1043s Finished ref gaps 1043s Finished read gaps 1043s Mutated reference genome to subject genome 1043s SNPs introduced: 9 1043s Reference gaps introduced: 3 1043s Read gaps introduced: 1 1043s Rearrangements introduced: 1 1043s Created read sampler 1043s Sampling 135 reads 1043s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1043s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1043s parsing sequence Sim.pm.1... 1043s parsing sequence Sim.pm.2... 1043s Parsed 81 reference bases 1043s *** Run 80 of 100 1043s /usr/bin/bowtie2 --score-min L,3.01095351527028,2.71916564513421 --rfg 38.1047241026077,8.05755824171587 -i S,2.89237312919075 -N 0 -L23 -D 35 --np 2 --large-index -k 2 --rdg 13.9552679141973 --mp 8.45629356232702,5.00935318544275 --local --cp-ival 3 --cp-min 9 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1043s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1043s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #2 of read '48' because it was < 2 characters long 1043s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1043s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1043s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #2 of read '59' because it was < 2 characters long 1043s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #2 of read '60' because it was < 2 characters long 1043s Read 50 alignments... 1043s Warning: skipping mate #1 of read '119' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read '119' because it was < 2 characters long 1043s Read 100 alignments... 1043s Read 150 alignments... 1043s Read 200 alignments... 1043s 135 reads; of these: 1043s 135 (100.00%) were paired; of these: 1043s 135 (100.00%) aligned concordantly 0 times 1043s 0 (0.00%) aligned concordantly exactly 1 time 1043s 0 (0.00%) aligned concordantly >1 times 1043s ---- 1043s 135 pairs aligned concordantly 0 times; of these: 1043s 0 (0.00%) aligned discordantly 1 time 1043s ---- 1043s 135 pairs aligned 0 times concordantly or discordantly; of these: 1043s 270 mates make up the pairs; of these: 1043s 270 (100.00%) aligned 0 times 1043s 0 (0.00%) aligned exactly 1 time 1043s 0 (0.00%) aligned >1 times 1043s 0.00% overall alignment rate 1043s Read 250 alignments... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s 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Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s Processing line... 1043s --- Summary --- 1043s Read 1 reference strings 1043s Checked 0 alignments, 0 edits 1043s --------------- 1043s PASSED 1043s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1043s /usr/bin/bowtie2 --score-min L,3.01095351527028,2.71916564513421 --rfg 38.1047241026077,8.05755824171587 -i S,2.89237312919075 -N 0 -L23 -D 35 --np 2 --large-index -k 2 --rdg 13.9552679141973 --mp 8.45629356232702,5.00935318544275 --local --cp-ival 3 --cp-min 9 -q -p 4 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1043s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1043s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1043s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1043s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #2 of read '48' because it was < 2 characters long 1043s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #2 of read '59' because it was < 2 characters long 1043s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #2 of read '60' because it was < 2 characters long 1043s Warning: skipping mate #1 of read '119' because length (1) <= # seed mismatches (0) 1043s Warning: skipping mate #1 of read '119' because it was < 2 characters long 1043s 135 reads; of these: 1043s 135 (100.00%) were paired; of these: 1043s 135 (100.00%) aligned concordantly 0 times 1043s 0 (0.00%) aligned concordantly exactly 1 time 1043s 0 (0.00%) aligned concordantly >1 times 1043s ---- 1043s 135 pairs aligned concordantly 0 times; of these: 1043s 0 (0.00%) aligned discordantly 1 time 1043s ---- 1043s 135 pairs aligned 0 times concordantly or discordantly; of these: 1043s 270 mates make up the pairs; of these: 1043s 270 (100.00%) aligned 0 times 1043s 0 (0.00%) aligned exactly 1 time 1043s 0 (0.00%) aligned >1 times 1043s 0.00% overall alignment rate 1043s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1043s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1043s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1043s Flattened IUPAC characters 1043s Mutating sequence Sim.pm.2 1043s Introducing 15 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1043s Finished SNPs 1043s Finished ref gaps 1043s Finished read gaps 1043s Mutating sequence Sim.pm.1 1043s Introducing 9 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1043s Finished SNPs 1043s Finished ref gaps 1043s Finished read gaps 1043s Mutated reference genome to subject genome 1043s SNPs introduced: 24 1043s Reference gaps introduced: 0 1043s Read gaps introduced: 1 1043s Rearrangements introduced: 1 1043s Created read sampler 1043s Sampling 136 reads 1043s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1043s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1043s parsing sequence Sim.pm.1... 1043s parsing sequence Sim.pm.2... 1043s Parsed 81 reference bases 1043s *** Run 81 of 100 1043s /usr/bin/bowtie2 --trim3 5 --mp 6.05738016910726,3.59072770607278 --ma 29.4719333979834 --large-index -M 3 --cp-min 12 --cp-ival 1 --mm --trim5 4 --rfg 5.03005265097808 --n-ceil 1.24916030800837,1.18874969638126 --score-min L,6.42480207845018,2.69139568217501 --norc -R 4 -D 14 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1043s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1043s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1043s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '1' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1043s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '2' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1043s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1043s Warning: skipping read '4' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1043s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '8' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1043s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '17' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1043s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 1043s Warning: skipping read '18' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1043s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '21' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1043s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '23' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1043s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '29' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1043s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '32' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1043s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '33' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1043s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '34' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1043s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '36' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1043s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '37' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1043s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '43' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1043s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '44' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1043s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '45' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1043s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 1043s Warning: skipping read '49' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1043s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '50' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1043s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1043s Warning: skipping read '52' because it was < 2 characters long 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1043s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1044s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '58' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1044s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '59' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1044s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '60' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1044s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '61' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1044s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '62' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1044s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '66' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1044s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '70' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1044s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '72' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1044s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '73' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1044s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '74' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1044s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '91' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1044s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '92' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1044s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '95' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1044s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '98' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1044s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '103' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1044s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '107' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1044s Warning: skipping read '123' because length (1) <= # seed mismatches (0) 1044s Warning: skipping read '123' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1044s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '124' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1044s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '125' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1044s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '131' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1044s 136 reads; of these: 1044s 136 (100.00%) were unpaired; of these: 1044s 126 (92.65%) aligned 0 times 1044s 3 (2.21%) aligned exactly 1 time 1044s 7 (5.15%) aligned >1 times 1044s 7.35% overall alignment rate 1044s Read 50 alignments... 1044s Read 100 alignments... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s AT 1044s AT 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s AT 1044s AT 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s GT 1044s GT 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s GG 1044s GG 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s GGA 1044s GGA 1044s Processing line... 1044s ACC 1044s ACC 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s CG 1044s CG 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s GT 1044s GT 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s TCCCGTAT 1044s TCCCGTAT 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s ACA 1044s ACA 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s --- Summary --- 1044s /usr/bin/bowtie2 --trim3 5 --mp 6.05738016910726,3.59072770607278 --ma 29.4719333979834 --large-index -M 3 --cp-min 12 --cp-ival 1 --mm --trim5 4 --rfg 5.03005265097808 --n-ceil 1.24916030800837,1.18874969638126 --score-min L,6.42480207845018,2.69139568217501 --norc -R 4 -D 14 -r -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1044s Read 1 reference strings 1044s Checked 10 alignments, 0 edits 1044s --------------- 1044s PASSED 1044s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1044s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1044s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1044s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '1' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1044s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '2' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1044s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1044s Warning: skipping read '4' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1044s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '8' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1044s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '17' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1044s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 1044s Warning: skipping read '18' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1044s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '21' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1044s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '23' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1044s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '29' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1044s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '32' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1044s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 1044s Warning: skipping read '49' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1044s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '50' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1044s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '52' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1044s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '58' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1044s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '59' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1044s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '60' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1044s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '61' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1044s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '62' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1044s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '66' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1044s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '70' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1044s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '72' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1044s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '73' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1044s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '74' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1044s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '33' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1044s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '34' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1044s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '36' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1044s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '37' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1044s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '43' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1044s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '44' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1044s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '45' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1044s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '98' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1044s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '103' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1044s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '107' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1044s Warning: skipping read '123' because length (1) <= # seed mismatches (0) 1044s Warning: skipping read '123' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1044s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '124' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1044s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '125' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1044s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '131' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1044s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '91' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1044s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '92' because it was < 2 characters long 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1044s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1044s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read '95' because it was < 2 characters long 1044s 136 reads; of these: 1044s 136 (100.00%) were unpaired; of these: 1044s 126 (92.65%) aligned 0 times 1044s 3 (2.21%) aligned exactly 1 time 1044s 7 (5.15%) aligned >1 times 1044s 7.35% overall alignment rate 1044s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1044s Flattened IUPAC characters 1044s Mutating sequence Sim.pm.2 1044s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1044s Finished SNPs 1044s Finished ref gaps 1044s Finished read gaps 1044s *** Run 82 of 100 1044s /usr/bin/bowtie2 --n-ceil 1.00357054863288,0.163622130364124 --large-index --score-min L,5.01238457628185,9.3286956408709 --trim3 6 --trim5 8 --local -N 1 -L31 --cp-ival 4 --mm --cp-min 6 -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta 1044s Mutating sequence Sim.pm.1 1044s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1044s Finished SNPs 1044s Finished ref gaps 1044s Finished read gaps 1044s Mutated reference genome to subject genome 1044s SNPs introduced: 8 1044s Reference gaps introduced: 1 1044s Read gaps introduced: 0 1044s Rearrangements introduced: 0 1044s Created read sampler 1044s Sampling 81 reads 1044s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1044s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1044s parsing sequence Sim.pm.1... 1044s parsing sequence Sim.pm.2... 1044s Parsed 81 reference bases 1044s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '3' because it was < 2 characters long 1044s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '5' because it was < 2 characters long 1044s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '7' because it was < 2 characters long 1044s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '8' because it was < 2 characters long 1044s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '10' because it was < 2 characters long 1044s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '11' because it was < 2 characters long 1044s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '12' because it was < 2 characters long 1044s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '13' because it was < 2 characters long 1044s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '24' because it was < 2 characters long 1044s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '25' because it was < 2 characters long 1044s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '29' because it was < 2 characters long 1044s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '31' because it was < 2 characters long 1044s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '34' because it was < 2 characters long 1044s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '35' because it was < 2 characters long 1044s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '36' because it was < 2 characters long 1044s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '38' because it was < 2 characters long 1044s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '40' because it was < 2 characters long 1044s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '42' because it was < 2 characters long 1044s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '45' because it was < 2 characters long 1044s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '47' because it was < 2 characters long 1044s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '49' because it was < 2 characters long 1044s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '54' because it was < 2 characters long 1044s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '55' because it was < 2 characters long 1044s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '56' because it was < 2 characters long 1044s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '57' because it was < 2 characters long 1044s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '63' because it was < 2 characters long 1044s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '67' because it was < 2 characters long 1044s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '73' because it was < 2 characters long 1044s Warning: skipping read '74' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '74' because it was < 2 characters long 1044s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '76' because it was < 2 characters long 1044s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '80' because it was < 2 characters long 1044s 81 reads; of these: 1044s 81 (100.00%) were unpaired; of these: 1044s 81 (100.00%) aligned 0 times 1044s 0 (0.00%) aligned exactly 1 time 1044s 0 (0.00%) aligned >1 times 1044s 0.00% overall alignment rate 1044s Read 50 alignments... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s --- Summary --- 1044s Read 1 reference strings 1044s Checked 0 alignments, 0 edits 1044s --------------- 1044s PASSED 1044s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1044s /usr/bin/bowtie2 --n-ceil 1.00357054863288,0.163622130364124 --large-index --score-min L,5.01238457628185,9.3286956408709 --trim3 6 --trim5 8 --local -N 1 -L31 --cp-ival 4 --mm --cp-min 6 -f -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1044s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '3' because it was < 2 characters long 1044s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '5' because it was < 2 characters long 1044s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '7' because it was < 2 characters long 1044s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '8' because it was < 2 characters long 1044s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '10' because it was < 2 characters long 1044s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '11' because it was < 2 characters long 1044s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '12' because it was < 2 characters long 1044s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '13' because it was < 2 characters long 1044s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '24' because it was < 2 characters long 1044s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '25' because it was < 2 characters long 1044s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '29' because it was < 2 characters long 1044s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '31' because it was < 2 characters long 1044s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '34' because it was < 2 characters long 1044s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '35' because it was < 2 characters long 1044s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '36' because it was < 2 characters long 1044s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '38' because it was < 2 characters long 1044s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '40' because it was < 2 characters long 1044s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '42' because it was < 2 characters long 1044s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '45' because it was < 2 characters long 1044s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '47' because it was < 2 characters long 1044s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '67' because it was < 2 characters long 1044s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '73' because it was < 2 characters long 1044s Warning: skipping read '74' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '74' because it was < 2 characters long 1044s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '76' because it was < 2 characters long 1044s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '80' because it was < 2 characters long 1044s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '49' because it was < 2 characters long 1044s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '54' because it was < 2 characters long 1044s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '55' because it was < 2 characters long 1044s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '56' because it was < 2 characters long 1044s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '57' because it was < 2 characters long 1044s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 1044s Warning: skipping read '63' because it was < 2 characters long 1044s 81 reads; of these: 1044s 81 (100.00%) were unpaired; of these: 1044s 81 (100.00%) aligned 0 times 1044s 0 (0.00%) aligned exactly 1 time 1044s 0 (0.00%) aligned >1 times 1044s 0.00% overall alignment rate 1044s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1044s Flattened IUPAC characters 1044s Mutating sequence Sim.pm.2 1044s Introducing 1 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1044s Finished SNPs 1044s Finished ref gaps 1044s Finished read gaps 1044s Mutating sequence Sim.pm.1 1044s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1044s Finished SNPs 1044s Finished ref gaps 1044s Finished read gaps 1044s Mutated reference genome to subject genome 1044s SNPs introduced: 7 1044s Reference gaps introduced: 0 1044s Read gaps introduced: 0 1044s Rearrangements introduced: 3 1044s Created read sampler 1044s Sampling 53 reads 1044s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1044s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1044s parsing sequence Sim.pm.1... 1044s parsing sequence Sim.pm.2... 1044s Parsed 81 reference bases 1044s *** Run 83 of 100 1044s /usr/bin/bowtie2 --large-index --score-min L,4.50659716271831,5.35614714644501 -k 9 --trim5 7 --trim3 4 -i C,2.0713077932881,5.33090134762536 --local --cp-ival 3 --cp-min 2 --np 1 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1044s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 1044s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 1044s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 1044s 53 reads; of these: 1044s 53 (100.00%) were unpaired; of these: 1044s 53 (100.00%) aligned 0 times 1044s 0 (0.00%) aligned exactly 1 time 1044s 0 (0.00%) aligned >1 times 1044s 0.00% overall alignment rate 1044s Read 50 alignments... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s Processing line... 1044s --- Summary --- 1044s Read 1 reference strings 1044s Checked 0 alignments, 0 edits 1044s --------------- 1044s PASSED 1044s Flattened IUPAC characters 1044s Mutating sequence Sim.pm.1 1044s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1044s Finished SNPs 1044s Finished ref gaps 1044s Finished read gaps 1044s Mutating sequence Sim.pm.2 1044s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1044s Finished SNPs 1044s Finished ref gaps 1044s Finished read gaps 1044s Mutated reference genome to subject genome 1044s SNPs introduced: 12 1044s Reference gaps introduced: 1 1044s Read gaps introduced: 0 1044s Rearrangements introduced: 0 1044s Created read sampler 1044s Sampling 177 reads 1044s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1044s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1044s parsing sequence Sim.pm.1... 1044s parsing sequence Sim.pm.2... 1044s Parsed 81 reference bases 1044s *** Run 84 of 100 1044s /usr/bin/bowtie2 --cp-min 13 --cp-ival 1 --rdg 24.9424996190297 --mp 4.9312866004926,1.82341237971096 --large-index --ma 21.2072381417338 --nofw -R 4 --rfg 46.7688570392099 --trim5 8 --score-min L,3.67834959396148,6.44937732498957 --n-ceil 0.326638221863773,0.788311468440329 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1045s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1045s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '2' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1045s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '5' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1045s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '18' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1045s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '28' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1045s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '29' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1045s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '37' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1045s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '43' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1045s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '47' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1045s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '50' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1045s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '54' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1045s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '55' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1045s Warning: skipping read '67' because length (1) <= # seed mismatches (0) 1045s Warning: skipping read '67' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1045s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '73' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1045s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 1045s Warning: skipping read '74' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1045s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '77' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1045s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '81' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1045s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '83' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1045s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '85' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1045s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '91' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1045s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '96' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1045s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '97' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1045s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '98' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1045s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '99' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1045s Warning: skipping read '100' because length (1) <= # seed mismatches (0) 1045s Warning: skipping read '100' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1045s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '101' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1045s Warning: skipping read '104' because length (1) <= # seed mismatches (0) 1045s Warning: skipping read '104' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1045s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '105' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1045s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '107' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1045s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '112' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1045s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '113' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1045s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '125' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1045s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '130' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1045s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '132' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 1045s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '140' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 1045s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '143' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 1045s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '152' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 1045s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '154' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 1045s Warning: skipping read '157' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '157' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 1045s Warning: skipping read '160' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '160' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 1045s Warning: skipping read '165' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '165' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 1045s Warning: skipping read '166' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '166' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 1045s Warning: skipping read '167' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '167' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 1045s Warning: skipping read '168' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '168' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 1045s Warning: skipping read '171' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '171' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 1045s Warning: skipping read '174' because length (1) <= # seed mismatches (0) 1045s Warning: skipping read '174' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 1045s Warning: skipping read '175' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '175' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 1045s Warning: skipping read '176' because length (0) <= # seed mismatches (0) 1045s Warning: skipping read '176' because it was < 2 characters long 1045s Read 50 alignments... 1045s Read 100 alignments... 1045s Read 150 alignments... 1045s 177 reads; of these: 1045s 177 (100.00%) were unpaired; of these: 1045s 158 (89.27%) aligned 0 times 1045s 9 (5.08%) aligned exactly 1 time 1045s 10 (5.65%) aligned >1 times 1045s 10.73% overall alignment rate 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s TCCCGTATCGCGT 1045s TCCCGTATCGCGT 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s ACCGAAA 1045s ACCGAAA 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s CGTATCG 1045s CGTATCG 1045s Processing line... 1045s Processing line... 1045s TGTTCACGTGGGCGA 1045s TGTTCACGTGGGCGA 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s CA 1045s CA 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s CGT 1045s CGT 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s GTGGGC 1045s GTGGGC 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s GAC 1045s GAC 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s CGG 1045s CGG 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s AA 1045s AA 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s ATGACAACCGAAAGA 1045s ATGACAACCGAAAGA 1045s Processing line... 1045s Processing line... 1045s TGACAACCGAAAGACGGACGTA 1045s TGACAACCGAAAGACGGACGTA 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s GG 1045s GG 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s TT 1045s TT 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s TA 1045s TA 1045s Processing line... 1045s GAA 1045s GAA 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s GG 1045s GG 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s TA 1045s TA 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s ATGACAACCGAAAGACGGA 1045s ATGACAACCGAAAGACGGA 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s --- Summary --- 1045s Read 1 reference strings 1045s Checked 19 alignments, 0 edits 1045s --------------- 1045s PASSED 1045s Flattened IUPAC characters 1045s Mutating sequence Sim.pm.1 1045s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1045s Finished SNPs 1045s Finished ref gaps 1045s Finished read gaps 1045s Mutating sequence Sim.pm.2 1045s Introducing 6 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1045s Finished SNPs 1045s Finished ref gaps 1045s Finished read gaps 1045s Mutated reference genome to subject genome 1045s SNPs introduced: 12 1045s Reference gaps introduced: 1 1045s Read gaps introduced: 2 1045s Rearrangements introduced: 0 1045s Created read sampler 1045s Sampling 66 reads 1045s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1045s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1045s parsing sequence Sim.pm.1... 1045s parsing sequence Sim.pm.2... 1045s Parsed 81 reference bases 1045s *** Run 85 of 100 1045s /usr/bin/bowtie2 --cp-min 8 --cp-ival 1 --mp 7.2585244341635,4.09099922363411 --trim3 3 --ma 4.8356790132973 --large-index --np 2 -N 1 -L31 -D 12 -R 2 --score-min L,1.46167252922531,2.75763444155405 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1045s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1045s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #2 of read '4' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1045s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1045s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #2 of read '21' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1045s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1045s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1045s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1045s Warning: skipping mate #2 of read '34' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1045s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1045s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1045s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1045s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1045s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '62' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1045s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1045s Read 50 alignments... 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1045s Read 100 alignments... 1045s 66 reads; of these: 1045s 60 (90.91%) were paired; of these: 1045s 59 (98.33%) aligned concordantly 0 times 1045s 1 (1.67%) aligned concordantly exactly 1 time 1045s 0 (0.00%) aligned concordantly >1 times 1045s ---- 1045s 59 pairs aligned concordantly 0 times; of these: 1045s 0 (0.00%) aligned discordantly 1 time 1045s ---- 1045s 59 pairs aligned 0 times concordantly or discordantly; of these: 1045s 118 mates make up the pairs; of these: 1045s 104 (88.14%) aligned 0 times 1045s 9 (7.63%) aligned exactly 1 time 1045s 5 (4.24%) aligned >1 times 1045s 6 (9.09%) were unpaired; of these: 1045s 6 (100.00%) aligned 0 times 1045s 0 (0.00%) aligned exactly 1 time 1045s 0 (0.00%) aligned >1 times 1045s 12.70% overall alignment rate 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s ACCGAAAGA 1045s ACCGAAAGA 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s GACAACC 1045s GACAACC 1045s Processing line... 1045s Processing line... 1045s CG 1045s CG 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s GACGG 1045s GACGG 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s ACCGAAAGACGGACG 1045s ACCGAAAGACGGACG 1045s Processing line... 1045s Processing line... 1045s AAAGA 1045s AAAGA 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s CGT 1045s CGT 1045s Processing line... 1045s Processing line... 1045s GG 1045s GG 1045s Processing line... 1045s Processing line... 1045s AAAGACGGACGT 1045s AAAGACGGACGT 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s ACCGAAAGAC 1045s ACCGAAAGAC 1045s Processing line... 1045s GAAAGACGGAC 1045s GAAAGACGGAC 1045s /usr/bin/bowtie2 --cp-min 8 --cp-ival 1 --mp 7.2585244341635,4.09099922363411 --trim3 3 --ma 4.8356790132973 --large-index --np 2 -N 1 -L31 -D 12 -R 2 --score-min L,1.46167252922531,2.75763444155405 -q -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1045s Processing line... 1045s AACCGAAAGACGG 1045s AACCGAAAGACGG 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s GTATCG 1045s GTATCG 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s CC 1045s CC 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s ACGGACGT 1045s ACGGACGT 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s CGAAAG 1045s CGAAAG 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s Processing line... 1045s --- Summary --- 1045s Read 1 reference strings 1045s Checked 16 alignments, 0 edits 1045s --------------- 1045s PASSED 1045s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1045s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1045s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #2 of read '4' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1045s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1045s Warning: skipping mate #2 of read '34' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1045s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1045s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #2 of read '21' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1045s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1045s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1045s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1045s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1045s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '62' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1045s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1045s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (1) 1045s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1045s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1046s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1046s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1046s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (1) 1046s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1046s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1046s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1046s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1046s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1046s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1046s 66 reads; of these: 1046s 60 (90.91%) were paired; of these: 1046s 59 (98.33%) aligned concordantly 0 times 1046s 1 (1.67%) aligned concordantly exactly 1 time 1046s 0 (0.00%) aligned concordantly >1 times 1046s ---- 1046s 59 pairs aligned concordantly 0 times; of these: 1046s 0 (0.00%) aligned discordantly 1 time 1046s ---- 1046s 59 pairs aligned 0 times concordantly or discordantly; of these: 1046s 118 mates make up the pairs; of these: 1046s 104 (88.14%) aligned 0 times 1046s 9 (7.63%) aligned exactly 1 time 1046s 5 (4.24%) aligned >1 times 1046s 6 (9.09%) were unpaired; of these: 1046s 6 (100.00%) aligned 0 times 1046s 0 (0.00%) aligned exactly 1 time 1046s 0 (0.00%) aligned >1 times 1046s 12.70% overall alignment rate 1046s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1046s Flattened IUPAC characters 1046s Mutating sequence Sim.pm.1 1046s Introducing 9 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1046s Finished SNPs 1046s Finished ref gaps 1046s Finished read gaps 1046s Mutating sequence Sim.pm.2 1046s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1046s Finished SNPs 1046s Finished ref gaps 1046s Finished read gaps 1046s Mutated reference genome to subject genome 1046s SNPs introduced: 11 1046s Reference gaps introduced: 0 1046s Read gaps introduced: 1 1046s Rearrangements introduced: 0 1046s Created read sampler 1046s Sampling 56 reads 1046s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1046s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1046s parsing sequence Sim.pm.1... 1046s parsing sequence Sim.pm.2... 1046s Parsed 81 reference bases 1046s *** Run 86 of 100 1046s /usr/bin/bowtie2 --score-min L,8.00896479178314,7.47761564869309 --trim5 6 -i C,2.43384310364568 --rfg 24.5333038644543 --nofw --np 4 --large-index --trim3 1 --mp 9.51981944832236,3.22417176051745 --local --mm --cp-ival 2 --cp-min 2 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1046s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '1' because it was < 2 characters long 1046s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '2' because it was < 2 characters long 1046s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '4' because it was < 2 characters long 1046s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '9' because it was < 2 characters long 1046s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '11' because it was < 2 characters long 1046s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '17' because it was < 2 characters long 1046s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '18' because it was < 2 characters long 1046s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '26' because it was < 2 characters long 1046s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '29' because it was < 2 characters long 1046s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '31' because it was < 2 characters long 1046s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '35' because it was < 2 characters long 1046s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '40' because it was < 2 characters long 1046s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '45' because it was < 2 characters long 1046s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '46' because it was < 2 characters long 1046s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '52' because it was < 2 characters long 1046s 56 reads; of these: 1046s 56 (100.00%) were unpaired; of these: 1046s 56 (100.00%) aligned 0 times 1046s 0 (0.00%) aligned exactly 1 time 1046s 0 (0.00%) aligned >1 times 1046s 0.00% overall alignment rate 1046s Read 50 alignments... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s /usr/bin/bowtie2 --score-min L,8.00896479178314,7.47761564869309 --trim5 6 -i C,2.43384310364568 --rfg 24.5333038644543 --nofw --np 4 --large-index --trim3 1 --mp 9.51981944832236,3.22417176051745 --local --mm --cp-ival 2 --cp-min 2 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s Processing line... 1046s --- Summary --- 1046s Read 1 reference strings 1046s Checked 0 alignments, 0 edits 1046s --------------- 1046s PASSED 1046s ALSO checking that bowtie2 and bowtie2-align match up 1046s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '1' because it was < 2 characters long 1046s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '2' because it was < 2 characters long 1046s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '4' because it was < 2 characters long 1046s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '9' because it was < 2 characters long 1046s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '11' because it was < 2 characters long 1046s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '17' because it was < 2 characters long 1046s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '18' because it was < 2 characters long 1046s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '26' because it was < 2 characters long 1046s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '29' because it was < 2 characters long 1046s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '31' because it was < 2 characters long 1046s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '35' because it was < 2 characters long 1046s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '40' because it was < 2 characters long 1046s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '45' because it was < 2 characters long 1046s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '46' because it was < 2 characters long 1046s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '52' because it was < 2 characters long 1046s 56 reads; of these: 1046s 56 (100.00%) were unpaired; of these: 1046s 56 (100.00%) aligned 0 times 1046s 0 (0.00%) aligned exactly 1 time 1046s 0 (0.00%) aligned >1 times 1046s 0.00% overall alignment rate 1046s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1046s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1046s /usr/bin/bowtie2 --score-min L,8.00896479178314,7.47761564869309 --trim5 6 -i C,2.43384310364568 --rfg 24.5333038644543 --nofw --np 4 --large-index --trim3 1 --mp 9.51981944832236,3.22417176051745 --local --mm --cp-ival 2 --cp-min 2 -r -p 2 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1046s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '1' because it was < 2 characters long 1046s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '2' because it was < 2 characters long 1046s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '4' because it was < 2 characters long 1046s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '9' because it was < 2 characters long 1046s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '11' because it was < 2 characters long 1046s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '17' because it was < 2 characters long 1046s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '18' because it was < 2 characters long 1046s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '26' because it was < 2 characters long 1046s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '29' because it was < 2 characters long 1046s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '31' because it was < 2 characters long 1046s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '35' because it was < 2 characters long 1046s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '40' because it was < 2 characters long 1046s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '52' because it was < 2 characters long 1046s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '45' because it was < 2 characters long 1046s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '46' because it was < 2 characters long 1046s 56 reads; of these: 1046s 56 (100.00%) were unpaired; of these: 1046s 56 (100.00%) aligned 0 times 1046s 0 (0.00%) aligned exactly 1 time 1046s 0 (0.00%) aligned >1 times 1046s 0.00% overall alignment rate 1046s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1046s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1046s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1046s /usr/bin/bowtie2 --score-min L,8.00896479178314,7.47761564869309 --trim5 6 -i C,2.43384310364568 --rfg 24.5333038644543 --nofw --np 4 --large-index --trim3 1 --mp 9.51981944832236,3.22417176051745 --local --mm --cp-ival 2 --cp-min 2 -r -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1046s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1046s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '1' because it was < 2 characters long 1046s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '2' because it was < 2 characters long 1046s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '4' because it was < 2 characters long 1046s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '9' because it was < 2 characters long 1046s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '11' because it was < 2 characters long 1046s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '17' because it was < 2 characters long 1046s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '18' because it was < 2 characters long 1046s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '26' because it was < 2 characters long 1046s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '29' because it was < 2 characters long 1046s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '31' because it was < 2 characters long 1046s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '35' because it was < 2 characters long 1046s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '40' because it was < 2 characters long 1046s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '45' because it was < 2 characters long 1046s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1046s Warning: skipping read '46' because it was < 2 characters long 1046s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1046s Warning: skipping read '52' because it was < 2 characters long 1046s 56 reads; of these: 1046s 56 (100.00%) were unpaired; of these: 1046s 56 (100.00%) aligned 0 times 1046s 0 (0.00%) aligned exactly 1 time 1046s 0 (0.00%) aligned >1 times 1046s 0.00% overall alignment rate 1046s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1046s Flattened IUPAC characters 1046s Mutating sequence Sim.pm.1 1046s Introducing 11 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1046s Finished SNPs 1046s Finished ref gaps 1046s Finished read gaps 1046s Mutating sequence Sim.pm.2 1046s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1046s Finished SNPs 1046s Finished ref gaps 1046s Finished read gaps 1046s Mutated reference genome to subject genome 1046s SNPs introduced: 18 1046s Reference gaps introduced: 1 1046s Read gaps introduced: 0 1046s Rearrangements introduced: 0 1046s Created read sampler 1046s Sampling 61 reads 1046s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1046s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1046s parsing sequence Sim.pm.1... 1046s parsing sequence Sim.pm.2... 1046s Parsed 81 reference bases 1046s *** Run 87 of 100 1046s /usr/bin/bowtie2 --local --trim5 8 -a --gbar 18 --score-min L,1.53543415177236,9.05215837174722 --n-ceil 0.66813783803569,0.275547094606563 --large-index --cp-min 4 --cp-ival 1 -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1047s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1047s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '7' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1047s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '40' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '58' because it was < 2 characters long 1047s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 1047s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1047s 61 reads; of these: 1047s 49 (80.33%) were paired; of these: 1047s 49 (100.00%) aligned concordantly 0 times 1047s 0 (0.00%) aligned concordantly exactly 1 time 1047s 0 (0.00%) aligned concordantly >1 times 1047s ---- 1047s 49 pairs aligned concordantly 0 times; of these: 1047s 0 (0.00%) aligned discordantly 1 time 1047s ---- 1047s 49 pairs aligned 0 times concordantly or discordantly; of these: 1047s 98 mates make up the pairs; of these: 1047s 98 (100.00%) aligned 0 times 1047s 0 (0.00%) aligned exactly 1 time 1047s 0 (0.00%) aligned >1 times 1047s 12 (19.67%) were unpaired; of these: 1047s 12 (100.00%) aligned 0 times 1047s 0 (0.00%) aligned exactly 1 time 1047s 0 (0.00%) aligned >1 times 1047s 0.00% overall alignment rate 1047s Read 50 alignments... 1047s Read 100 alignments... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s --- Summary --- 1047s Read 1 reference strings 1047s Checked 0 alignments, 0 edits 1047s --------------- 1047s PASSED 1047s Flattened IUPAC characters 1047s Mutating sequence Sim.pm.2 1047s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1047s Finished SNPs 1047s Finished ref gaps 1047s Finished read gaps 1047s Mutating sequence Sim.pm.1 1047s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1047s Finished SNPs 1047s Finished ref gaps 1047s Finished read gaps 1047s Mutated reference genome to subject genome 1047s SNPs introduced: 8 1047s Reference gaps introduced: 1 1047s Read gaps introduced: 0 1047s Rearrangements introduced: 0 1047s Created read sampler 1047s Sampling 114 reads 1047s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1047s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1047s parsing sequence Sim.pm.1... 1047s parsing sequence Sim.pm.2... 1047s Parsed 81 reference bases 1047s *** Run 88 of 100 1047s /usr/bin/bowtie2 --cp-ival 1 --np 5 --cp-min 7 --gbar 4 --score-min L,2.69860301277659,3.60859609708687 --large-index --rfg 22.9884424922139 --trim3 5 --mp 9.3818778169619,8.88307615418987 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1047s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '3' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1047s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '12' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1047s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '18' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1047s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '21' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1047s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '31' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1047s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '40' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1047s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '45' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1047s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '46' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1047s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '47' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1047s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1047s Warning: skipping read '52' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1047s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 1047s Warning: skipping read '74' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1047s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '78' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1047s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '91' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1047s Warning: skipping read '97' because length (1) <= # seed mismatches (0) 1047s Warning: skipping read '97' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1047s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '99' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1047s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '104' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1047s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '106' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1047s Warning: skipping read '108' because length (1) <= # seed mismatches (0) 1047s Warning: skipping read '108' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1047s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 1047s Warning: skipping read '109' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1047s 114 reads; of these: 1047s 114 (100.00%) were unpaired; of these: 1047s 91 (79.82%) aligned 0 times 1047s 12 (10.53%) aligned exactly 1 time 1047s 11 (9.65%) aligned >1 times 1047s 20.18% overall alignment rate 1047s Read 50 alignments... 1047s Read 100 alignments... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s AGACGGAC 1047s AGACGGAC 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s TCACG 1047s TCACG 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s GTGG 1047s GTGG 1047s Processing line... 1047s ATCC 1047s ATCC 1047s Processing line... 1047s Processing line... 1047s AAAGACGGACGTA 1047s AAAGACGGACGTA 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s CGTA 1047s CGTA 1047s Processing line... 1047s Processing line... 1047s ACCGAAAGACGGACGT 1047s ACCGAAAGACGGACGT 1047s Processing line... 1047s CCCGT 1047s CCCGT 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s GATGACAACCGAA 1047s GATGACAACCGAA 1047s Processing line... 1047s AA 1047s AA 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s TGTTCA 1047s TGTTCA 1047s Processing line... 1047s Processing line... 1047s CCCGTAT 1047s CCCGTAT 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s TCACGT 1047s TCACGT 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s CC 1047s CC 1047s Processing line... 1047s Processing line... 1047s ATGACA 1047s ATGACA 1047s Processing line... 1047s CGAAAGACGGACG 1047s CGAAAGACGGACG 1047s Processing line... 1047s GAC 1047s GAC 1047s Processing line... 1047s TA 1047s TA 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s CAACCGAAAGACGGAC 1047s CAACCGAAAGACGGAC 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s GACGGAC 1047s GACGGAC 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s AT 1047s AT 1047s Processing line... 1047s ACGT 1047s ACGT 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s GAA 1047s GAA 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s Processing line... 1047s --- Summary --- 1047s Read 1 reference strings 1047s Checked 23 alignments, 0 edits 1047s --------------- 1047s PASSED 1047s ALSO checking that bowtie2 and bowtie2-align match up 1047s /usr/bin/bowtie2 --cp-ival 1 --np 5 --cp-min 7 --gbar 4 --score-min L,2.69860301277659,3.60859609708687 --large-index --rfg 22.9884424922139 --trim3 5 --mp 9.3818778169619,8.88307615418987 -r -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1047s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '3' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1047s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '12' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1047s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '18' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1047s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '21' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1047s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '31' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1047s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '40' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1047s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '45' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1047s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '46' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1047s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '47' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1047s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1047s Warning: skipping read '52' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1047s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 1047s Warning: skipping read '74' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1047s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '78' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1047s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '91' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1047s Warning: skipping read '97' because length (1) <= # seed mismatches (0) 1047s Warning: skipping read '97' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1047s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '99' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1047s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '104' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1047s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1047s Warning: skipping read '106' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1047s Warning: skipping read '108' because length (1) <= # seed mismatches (0) 1047s Warning: skipping read '108' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1047s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 1047s Warning: skipping read '109' because it was < 2 characters long 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1047s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1047s 114 reads; of these: 1047s 114 (100.00%) were unpaired; of these: 1047s 91 (79.82%) aligned 0 times 1047s 12 (10.53%) aligned exactly 1 time 1047s 11 (9.65%) aligned >1 times 1047s 20.18% overall alignment rate 1047s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1047s /usr/bin/bowtie2 --cp-ival 1 --np 5 --cp-min 7 --gbar 4 --score-min L,2.69860301277659,3.60859609708687 --large-index --rfg 22.9884424922139 --trim3 5 --mp 9.3818778169619,8.88307615418987 -r -p 3 -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1047s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1048s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '3' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1048s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '12' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1048s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '18' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1048s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '21' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1048s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '31' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1048s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1048s Warning: skipping read '52' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1048s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '91' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1048s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 1048s Warning: skipping read '74' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1048s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '78' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1048s Warning: skipping read '97' because length (1) <= # seed mismatches (0) 1048s Warning: skipping read '97' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1048s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '99' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1048s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '40' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1048s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '45' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1048s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '46' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1048s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '47' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1048s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '104' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1048s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '106' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1048s Warning: skipping read '108' because length (1) <= # seed mismatches (0) 1048s Warning: skipping read '108' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1048s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 1048s Warning: skipping read '109' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1048s 114 reads; of these: 1048s 114 (100.00%) were unpaired; of these: 1048s 91 (79.82%) aligned 0 times 1048s 12 (10.53%) aligned exactly 1 time 1048s 11 (9.65%) aligned >1 times 1048s 20.18% overall alignment rate 1048s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1048s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1048s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1048s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1048s /usr/bin/bowtie2 --cp-ival 1 --np 5 --cp-min 7 --gbar 4 --score-min L,2.69860301277659,3.60859609708687 --large-index --rfg 22.9884424922139 --trim3 5 --mp 9.3818778169619,8.88307615418987 -r -p 4 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1048s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '3' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1048s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '12' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1048s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1048s Warning: skipping read '52' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1048s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '18' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1048s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '21' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1048s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '31' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1048s Warning: skipping read '97' because length (1) <= # seed mismatches (0) 1048s Warning: skipping read '97' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1048s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '99' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1048s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '104' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1048s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '106' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1048s Warning: skipping read '108' because length (1) <= # seed mismatches (0) 1048s Warning: skipping read '108' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1048s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 1048s Warning: skipping read '74' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1048s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '78' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1048s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '40' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1048s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '45' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1048s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '46' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1048s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '47' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1048s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 1048s Warning: skipping read '109' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1048s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1048s Warning: skipping read '91' because it was < 2 characters long 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1048s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1048s 114 reads; of these: 1048s 114 (100.00%) were unpaired; of these: 1048s 91 (79.82%) aligned 0 times 1048s 12 (10.53%) aligned exactly 1 time 1048s 11 (9.65%) aligned >1 times 1048s 20.18% overall alignment rate 1048s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1048s Flattened IUPAC characters 1048s Mutating sequence Sim.pm.2 1048s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1048s Finished SNPs 1048s Finished ref gaps 1048s Finished read gaps 1048s Mutating sequence Sim.pm.1 1048s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1048s Finished SNPs 1048s Finished ref gaps 1048s Finished read gaps 1048s Mutated reference genome to subject genome 1048s SNPs introduced: 4 1048s Reference gaps introduced: 0 1048s Read gaps introduced: 1 1048s Rearrangements introduced: 1 1048s Created read sampler 1048s Sampling 61 reads 1048s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1048s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1048s parsing sequence Sim.pm.1... 1048s parsing sequence Sim.pm.2... 1048s Parsed 81 reference bases 1048s *** Run 89 of 100 1048s /usr/bin/bowtie2 --local -a --large-index --cp-min 7 --mm --cp-ival 1 -i C,2.92433368208276 --score-min L,1.55253903938728,2.18301712887197 --np 4 --qseq -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq 1048s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 1048s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1048s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 1048s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1048s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 1048s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1048s 61 reads; of these: 1048s 61 (100.00%) were paired; of these: 1048s 61 (100.00%) aligned concordantly 0 times 1048s 0 (0.00%) aligned concordantly exactly 1 time 1048s 0 (0.00%) aligned concordantly >1 times 1048s ---- 1048s 61 pairs aligned concordantly 0 times; of these: 1048s 0 (0.00%) aligned discordantly 1 time 1048s ---- 1048s 61 pairs aligned 0 times concordantly or discordantly; of these: 1048s 122 mates make up the pairs; of these: 1048s 122 (100.00%) aligned 0 times 1048s 0 (0.00%) aligned exactly 1 time 1048s 0 (0.00%) aligned >1 times 1048s 0.00% overall alignment rate 1048s Read 50 alignments... 1048s Read 100 alignments... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s /usr/bin/bowtie2 --local -a --large-index --cp-min 7 --mm --cp-ival 1 -i C,2.92433368208276 --score-min L,1.55253903938728,2.18301712887197 --np 4 --qseq -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.qseq -2 /tmp/Sim.pm.rtAHg7h8_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s Processing line... 1048s --- Summary --- 1048s Read 1 reference strings 1048s Checked 0 alignments, 0 edits 1048s --------------- 1048s PASSED 1048s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1049s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1049s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 1049s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1049s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1049s 61 reads; of these: 1049s 61 (100.00%) were paired; of these: 1049s 61 (100.00%) aligned concordantly 0 times 1049s 0 (0.00%) aligned concordantly exactly 1 time 1049s 0 (0.00%) aligned concordantly >1 times 1049s ---- 1049s 61 pairs aligned concordantly 0 times; of these: 1049s 0 (0.00%) aligned discordantly 1 time 1049s ---- 1049s 61 pairs aligned 0 times concordantly or discordantly; of these: 1049s 122 mates make up the pairs; of these: 1049s 122 (100.00%) aligned 0 times 1049s 0 (0.00%) aligned exactly 1 time 1049s 0 (0.00%) aligned >1 times 1049s 0.00% overall alignment rate 1049s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1049s Flattened IUPAC characters 1049s Mutating sequence Sim.pm.2 1049s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1049s Finished SNPs 1049s Finished ref gaps 1049s Finished read gaps 1049s Mutating sequence Sim.pm.1 1049s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1049s Finished SNPs 1049s Finished ref gaps 1049s Finished read gaps 1049s Mutated reference genome to subject genome 1049s SNPs introduced: 12 1049s Reference gaps introduced: 0 1049s Read gaps introduced: 1 1049s Rearrangements introduced: 0 1049s Created read sampler 1049s Sampling 119 reads 1049s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1049s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1049s parsing sequence Sim.pm.1... 1049s *** Run 90 of 100 1049s /usr/bin/bowtie2 --cp-min 3 --cp-ival 4 --mp 5.30605802685718,3.62785448011366 --trim3 8 --local --large-index -M 4 --np 2 --rfg 35.2726806514793,11.9794933308181 --n-ceil 0.0732513930305692,1.11175031005348 --score-min L,3.6285004356981,8.1920988347048 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1049s parsing sequence Sim.pm.2... 1049s Parsed 81 reference bases 1049s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1049s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1049s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 1049s Warning: skipping read '19' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '21' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '48' because it was < 2 characters long 1049s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1049s Warning: skipping read '52' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '58' because it was < 2 characters long 1049s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1049s Warning: skipping read '61' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1049s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1049s Warning: skipping read '72' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #2 of read '74' because length (1) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '74' because it was < 2 characters long 1049s Warning: skipping mate #2 of read '74' because it was < 2 characters long 1049s Read 50 alignments... 1049s Warning: skipping mate #2 of read '84' because length (1) <= # seed mismatches (0) 1049s Warning: skipping mate #2 of read '84' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '87' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '88' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '93' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1049s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 1049s Warning: skipping read '108' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '111' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1049s Read 100 alignments... 1049s 119 reads; of these: 1049s 99 (83.19%) were paired; of these: 1049s 99 (100.00%) aligned concordantly 0 times 1049s 0 (0.00%) aligned concordantly exactly 1 time 1049s 0 (0.00%) aligned concordantly >1 times 1049s ---- 1049s 99 pairs aligned concordantly 0 times; of these: 1049s 0 (0.00%) aligned discordantly 1 time 1049s ---- 1049s 99 pairs aligned 0 times concordantly or discordantly; of these: 1049s 198 mates make up the pairs; of these: 1049s 198 (100.00%) aligned 0 times 1049s 0 (0.00%) aligned exactly 1 time 1049s 0 (0.00%) aligned >1 times 1049s 20 (16.81%) were unpaired; of these: 1049s 20 (100.00%) aligned 0 times 1049s 0 (0.00%) aligned exactly 1 time 1049s 0 (0.00%) aligned >1 times 1049s 0.00% overall alignment rate 1049s Read 150 alignments... 1049s Read 200 alignments... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing 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line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s /usr/bin/bowtie2 --cp-min 3 --cp-ival 4 --mp 5.30605802685718,3.62785448011366 --trim3 8 --local --large-index -M 4 --np 2 --rfg 35.2726806514793,11.9794933308181 --n-ceil 0.0732513930305692,1.11175031005348 --score-min L,3.6285004356981,8.1920988347048 -r -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s Processing line... 1049s --- Summary --- 1049s Read 1 reference strings 1049s Checked 0 alignments, 0 edits 1049s --------------- 1049s PASSED 1049s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1049s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1049s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1049s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 1049s Warning: skipping read '19' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '21' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '48' because it was < 2 characters long 1049s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1049s Warning: skipping read '52' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '58' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1049s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1049s Warning: skipping read '72' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #2 of read '74' because length (1) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '74' because it was < 2 characters long 1049s Warning: skipping mate #2 of read '74' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1049s Warning: skipping mate #2 of read '84' because length (1) <= # seed mismatches (0) 1049s Warning: skipping mate #2 of read '84' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '87' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '88' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1049s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1049s Warning: skipping read '61' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '93' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1049s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 1049s Warning: skipping read '108' because it was < 2 characters long 1049s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 1049s Warning: skipping mate #1 of read '111' because it was < 2 characters long 1049s 119 reads; of these: 1049s 99 (83.19%) were paired; of these: 1049s 99 (100.00%) aligned concordantly 0 times 1049s 0 (0.00%) aligned concordantly exactly 1 time 1049s 0 (0.00%) aligned concordantly >1 times 1049s ---- 1049s 99 pairs aligned concordantly 0 times; of these: 1049s 0 (0.00%) aligned discordantly 1 time 1049s ---- 1049s 99 pairs aligned 0 times concordantly or discordantly; of these: 1049s 198 mates make up the pairs; of these: 1049s 198 (100.00%) aligned 0 times 1049s 0 (0.00%) aligned exactly 1 time 1049s 0 (0.00%) aligned >1 times 1049s 20 (16.81%) were unpaired; of these: 1049s 20 (100.00%) aligned 0 times 1049s 0 (0.00%) aligned exactly 1 time 1049s 0 (0.00%) aligned >1 times 1049s 0.00% overall alignment rate 1049s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1049s Flattened IUPAC characters 1049s Mutating sequence Sim.pm.1 1049s Introducing 9 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1049s Finished SNPs 1049s Finished ref gaps 1049s Finished read gaps 1049s Mutating sequence Sim.pm.2 1049s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1049s Finished SNPs 1049s Finished ref gaps 1049s Finished read gaps 1049s Mutated reference genome to subject genome 1049s SNPs introduced: 9 1049s Reference gaps introduced: 0 1049s Read gaps introduced: 1 1049s Rearrangements introduced: 2 1049s Created read sampler 1049s Sampling 68 reads 1049s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1049s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1049s parsing sequence Sim.pm.1... 1049s parsing sequence Sim.pm.2... 1049s Parsed 81 reference bases 1049s *** Run 91 of 100 1049s /usr/bin/bowtie2 --large-index --score-min L,2.11063451385309,3.72749188115672 --rdg 23.585997993038 --local --cp-ival 1 --cp-min 2 -f -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta 1050s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1050s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1050s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 1050s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1050s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 1050s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1050s Read 50 alignments... 1050s Read 100 alignments... 1050s 68 reads; of these: 1050s 68 (100.00%) were paired; of these: 1050s 68 (100.00%) aligned concordantly 0 times 1050s 0 (0.00%) aligned concordantly exactly 1 time 1050s 0 (0.00%) aligned concordantly >1 times 1050s ---- 1050s 68 pairs aligned concordantly 0 times; of these: 1050s 0 (0.00%) aligned discordantly 1 time 1050s ---- 1050s 68 pairs aligned 0 times concordantly or discordantly; of these: 1050s 136 mates make up the pairs; of these: 1050s 136 (100.00%) aligned 0 times 1050s 0 (0.00%) aligned exactly 1 time 1050s 0 (0.00%) aligned >1 times 1050s 0.00% overall alignment rate 1050s Processing line... 1050s /usr/bin/bowtie2 --large-index --score-min L,2.11063451385309,3.72749188115672 --rdg 23.585997993038 --local --cp-ival 1 --cp-min 2 -f -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s Processing line... 1050s --- Summary --- 1050s Read 1 reference strings 1050s Checked 0 alignments, 0 edits 1050s --------------- 1050s PASSED 1050s ALSO checking that bowtie2 and bowtie2-align match up 1050s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1050s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1050s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 1050s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1050s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 1050s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1050s 68 reads; of these: 1050s 68 (100.00%) were paired; of these: 1050s 68 (100.00%) aligned concordantly 0 times 1050s 0 (0.00%) aligned concordantly exactly 1 time 1050s 0 (0.00%) aligned concordantly >1 times 1050s ---- 1050s 68 pairs aligned concordantly 0 times; of these: 1050s 0 (0.00%) aligned discordantly 1 time 1050s ---- 1050s 68 pairs aligned 0 times concordantly or discordantly; of these: 1050s 136 mates make up the pairs; of these: 1050s 136 (100.00%) aligned 0 times 1050s 0 (0.00%) aligned exactly 1 time 1050s 0 (0.00%) aligned >1 times 1050s 0.00% overall alignment rate 1050s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1050s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1050s /usr/bin/bowtie2 --large-index --score-min L,2.11063451385309,3.72749188115672 --rdg 23.585997993038 --local --cp-ival 1 --cp-min 2 -f -p 4 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1050s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1050s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1050s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 1050s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1050s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 1050s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1050s 68 reads; of these: 1050s 68 (100.00%) were paired; of these: 1050s 68 (100.00%) aligned concordantly 0 times 1050s 0 (0.00%) aligned concordantly exactly 1 time 1050s 0 (0.00%) aligned concordantly >1 times 1050s ---- 1050s 68 pairs aligned concordantly 0 times; of these: 1050s 0 (0.00%) aligned discordantly 1 time 1050s ---- 1050s 68 pairs aligned 0 times concordantly or discordantly; of these: 1050s 136 mates make up the pairs; of these: 1050s 136 (100.00%) aligned 0 times 1050s 0 (0.00%) aligned exactly 1 time 1050s 0 (0.00%) aligned >1 times 1050s 0.00% overall alignment rate 1050s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1050s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1050s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1050s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1050s /usr/bin/bowtie2 --large-index --score-min L,2.11063451385309,3.72749188115672 --rdg 23.585997993038 --local --cp-ival 1 --cp-min 2 -f -p 2 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1051s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1051s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1051s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 1051s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1051s 68 reads; of these: 1051s 68 (100.00%) were paired; of these: 1051s 68 (100.00%) aligned concordantly 0 times 1051s 0 (0.00%) aligned concordantly exactly 1 time 1051s 0 (0.00%) aligned concordantly >1 times 1051s ---- 1051s 68 pairs aligned concordantly 0 times; of these: 1051s 0 (0.00%) aligned discordantly 1 time 1051s ---- 1051s 68 pairs aligned 0 times concordantly or discordantly; of these: 1051s 136 mates make up the pairs; of these: 1051s 136 (100.00%) aligned 0 times 1051s 0 (0.00%) aligned exactly 1 time 1051s 0 (0.00%) aligned >1 times 1051s 0.00% overall alignment rate 1051s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1051s Flattened IUPAC characters 1051s Mutating sequence Sim.pm.1 1051s Introducing 4 SNPs, 0/1 ref/read gaps, and 2 rearrangements 1051s Finished SNPs 1051s Finished ref gaps 1051s Finished read gaps 1051s Mutating sequence Sim.pm.2 1051s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1051s Finished SNPs 1051s Finished ref gaps 1051s Finished read gaps 1051s Mutated reference genome to subject genome 1051s SNPs introduced: 11 1051s Reference gaps introduced: 0 1051s Read gaps introduced: 2 1051s Rearrangements introduced: 2 1051s Created read sampler 1051s Sampling 46 reads 1051s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1051s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1051s parsing sequence Sim.pm.1... 1051s parsing sequence Sim.pm.2... 1051s Parsed 81 reference bases 1051s *** Run 92 of 100 1051s /usr/bin/bowtie2 -a --large-index --cp-min 3 --cp-ival 3 --rfg 30.1400758437377 -i S,0.864469563811977 --trim5 8 --score-min L,6.42245773547744,5.13615383793278 --np 6 --nofw -D 36 -q -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fastq 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1051s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '1' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1051s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '5' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1051s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '8' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1051s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '18' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1051s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '19' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1051s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '25' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1051s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '27' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1051s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '30' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1051s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '39' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1051s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '44' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1051s 46 reads; of these: 1051s 46 (100.00%) were unpaired; of these: 1051s 45 (97.83%) aligned 0 times 1051s 1 (2.17%) aligned exactly 1 time 1051s 0 (0.00%) aligned >1 times 1051s 2.17% overall alignment rate 1051s Read 50 alignments... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s ATGACAACCGAAAGACGGA 1051s ATGACAACCGAAAGACGGA 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s --- Summary --- 1051s Read 1 reference strings 1051s Checked 1 alignments, 0 edits 1051s --------------- 1051s PASSED 1051s Flattened IUPAC characters 1051s Mutating sequence Sim.pm.2 1051s Introducing 2 SNPs, 0/1 ref/read gaps, and 3 rearrangements 1051s Finished SNPs 1051s Finished ref gaps 1051s Finished read gaps 1051s Mutating sequence Sim.pm.1 1051s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1051s Finished SNPs 1051s Finished ref gaps 1051s Finished read gaps 1051s Mutated reference genome to subject genome 1051s SNPs introduced: 7 1051s Reference gaps introduced: 0 1051s Read gaps introduced: 2 1051s Rearrangements introduced: 3 1051s Created read sampler 1051s Sampling 125 reads 1051s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1051s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1051s parsing sequence Sim.pm.1... 1051s parsing sequence Sim.pm.2... 1051s *** Run 93 of 100 1051s /usr/bin/bowtie2 --score-min L,6.01657718858172,3.91794184643079 --rfg 40.2149978933273,10.2980754921848 --np 4 --norc -M 3 --large-index --trim3 6 --mp 7.89383159809545,1.70614867798176 --cp-ival 1 --mm --cp-min 7 -f -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta 1051s Parsed 81 reference bases 1051s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1051s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '7' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1051s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1051s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 1051s Warning: skipping mate #2 of read '16' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1051s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1051s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1051s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 1051s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1051s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 1051s Warning: skipping read '32' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1051s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1051s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1051s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 1051s Warning: skipping mate #2 of read '60' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1051s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1051s Read 50 alignments... 1051s Read 100 alignments... 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1051s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1051s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1051s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1051s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1051s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1051s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '86' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1051s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '90' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1051s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1051s Warning: skipping read '98' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1051s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '106' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1051s Read 150 alignments... 1051s Read 200 alignments... 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1051s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '118' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1051s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 1051s Warning: skipping mate #1 of read '120' because it was < 2 characters long 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 1051s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1051s 125 reads; of these: 1051s 113 (90.40%) were paired; of these: 1051s 113 (100.00%) aligned concordantly 0 times 1051s 0 (0.00%) aligned concordantly exactly 1 time 1051s 0 (0.00%) aligned concordantly >1 times 1051s ---- 1051s 113 pairs aligned concordantly 0 times; of these: 1051s 0 (0.00%) aligned discordantly 1 time 1051s ---- 1051s 113 pairs aligned 0 times concordantly or discordantly; of these: 1051s 226 mates make up the pairs; of these: 1051s 212 (93.81%) aligned 0 times 1051s 6 (2.65%) aligned exactly 1 time 1051s 8 (3.54%) aligned >1 times 1051s 12 (9.60%) were unpaired; of these: 1051s 12 (100.00%) aligned 0 times 1051s 0 (0.00%) aligned exactly 1 time 1051s 0 (0.00%) aligned >1 times 1051s 5.88% overall alignment rate 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s TCCTGTTCACGTGGGCGAC 1051s TCCTGTTCACGTGGGCGAC 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s GATGACA 1051s GATGACA 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s CCGTAT 1051s CCGTAT 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s GA 1051s GA 1051s Processing line... 1051s Processing line... 1051s AA 1051s AA 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s AACCGAAAGACGGACGT 1051s AACCGAAAGACGGACGT 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s CGT 1051s CGT 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s TCCCGTA 1051s TCCCGTA 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s GAAA 1051s GAAA 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s TGG 1051s TGG 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s CGTA 1051s CGTA 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s GAAAGACGG 1051s GAAAGACGG 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s CCCGTATCGC 1051s CCCGTATCGC 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s AC 1051s AC 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s Processing line... 1051s --- Summary --- 1051s Read 1 reference strings 1051s Checked 14 alignments, 0 edits 1051s --------------- 1051s PASSED 1051s ALSO checking that bowtie2 and bowtie2-align match up 1051s /usr/bin/bowtie2 --score-min L,6.01657718858172,3.91794184643079 --rfg 40.2149978933273,10.2980754921848 --np 4 --norc -M 3 --large-index --trim3 6 --mp 7.89383159809545,1.70614867798176 --cp-ival 1 --mm --cp-min 7 -f -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.als 1052s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1052s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '7' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1052s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1052s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #2 of read '16' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1052s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1052s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1052s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1052s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 1052s Warning: skipping read '32' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1052s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1052s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1052s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #2 of read '60' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1052s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1052s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1052s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1052s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1052s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1052s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1052s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '86' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1052s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '90' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1052s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1052s Warning: skipping read '98' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1052s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '106' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1052s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '118' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1052s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '120' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1052s 125 reads; of these: 1052s 113 (90.40%) were paired; of these: 1052s 113 (100.00%) aligned concordantly 0 times 1052s 0 (0.00%) aligned concordantly exactly 1 time 1052s 0 (0.00%) aligned concordantly >1 times 1052s ---- 1052s 113 pairs aligned concordantly 0 times; of these: 1052s 0 (0.00%) aligned discordantly 1 time 1052s ---- 1052s 113 pairs aligned 0 times concordantly or discordantly; of these: 1052s 226 mates make up the pairs; of these: 1052s 212 (93.81%) aligned 0 times 1052s 6 (2.65%) aligned exactly 1 time 1052s 8 (3.54%) aligned >1 times 1052s 12 (9.60%) were unpaired; of these: 1052s 12 (100.00%) aligned 0 times 1052s 0 (0.00%) aligned exactly 1 time 1052s 0 (0.00%) aligned >1 times 1052s 5.88% overall alignment rate 1052s diff -uw /tmp/Sim.pm.rtAHg7h8.als /tmp/Sim.pm.rtAHg7h8.debug.als 1052s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1052s /usr/bin/bowtie2 --score-min L,6.01657718858172,3.91794184643079 --rfg 40.2149978933273,10.2980754921848 --np 4 --norc -M 3 --large-index --trim3 6 --mp 7.89383159809545,1.70614867798176 --cp-ival 1 --mm --cp-min 7 -f -p 2 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1052s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1052s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1052s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '7' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1052s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1052s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #2 of read '16' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1052s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1052s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1052s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 1052s Warning: skipping read '32' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1052s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1052s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #2 of read '60' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1052s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1052s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1052s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1052s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1052s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1052s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1052s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1052s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '86' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1052s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '90' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1052s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1052s Warning: skipping read '98' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1052s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '106' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1052s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '118' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1052s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '120' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1052s 125 reads; of these: 1052s 113 (90.40%) were paired; of these: 1052s 113 (100.00%) aligned concordantly 0 times 1052s 0 (0.00%) aligned concordantly exactly 1 time 1052s 0 (0.00%) aligned concordantly >1 times 1052s ---- 1052s 113 pairs aligned concordantly 0 times; of these: 1052s 0 (0.00%) aligned discordantly 1 time 1052s ---- 1052s 113 pairs aligned 0 times concordantly or discordantly; of these: 1052s 226 mates make up the pairs; of these: 1052s 212 (93.81%) aligned 0 times 1052s 6 (2.65%) aligned exactly 1 time 1052s 8 (3.54%) aligned >1 times 1052s 12 (9.60%) were unpaired; of these: 1052s 12 (100.00%) aligned 0 times 1052s 0 (0.00%) aligned exactly 1 time 1052s 0 (0.00%) aligned >1 times 1052s 5.88% overall alignment rate 1052s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1052s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1052s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1052s Flattened IUPAC characters 1052s Mutating sequence Sim.pm.1 1052s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1052s Finished SNPs 1052s Finished ref gaps 1052s Finished read gaps 1052s Mutating sequence Sim.pm.2 1052s Introducing 1 SNPs, 1/1 ref/read gaps, and 1 rearrangements 1052s Finished SNPs 1052s Finished ref gaps 1052s Finished read gaps 1052s Mutated reference genome to subject genome 1052s SNPs introduced: 5 1052s Reference gaps introduced: 2 1052s Read gaps introduced: 1 1052s Rearrangements introduced: 2 1052s Created read sampler 1052s Sampling 91 reads 1052s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fastq & /tmp/Sim.pm.rtAHg7h8_2.fastq 1052s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1052s parsing sequence Sim.pm.1... 1052s parsing sequence Sim.pm.2... 1052s Parsed 81 reference bases 1052s *** Run 94 of 100 1052s /usr/bin/bowtie2 --large-index --score-min L,7.82044783175833,9.61442281642274 --trim5 2 -a --mp 3.57372232422531,2.51205956354973 --cp-ival 1 -R 4 --cp-min 4 --np 2 --nofw -q -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1052s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1052s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1052s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1052s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1052s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #2 of read '41' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1052s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #1 of read '54' because it was < 2 characters long 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1052s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 1052s Warning: skipping mate #2 of read '65' because it was < 2 characters long 1052s Read 50 alignments... 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1052s Read 100 alignments... 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1052s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1052s 91 reads; of these: 1052s 86 (94.51%) were paired; of these: 1052s 86 (100.00%) aligned concordantly 0 times 1052s 0 (0.00%) aligned concordantly exactly 1 time 1052s 0 (0.00%) aligned concordantly >1 times 1052s ---- 1052s 86 pairs aligned concordantly 0 times; of these: 1052s 0 (0.00%) aligned discordantly 1 time 1052s ---- 1052s 86 pairs aligned 0 times concordantly or discordantly; of these: 1052s 172 mates make up the pairs; of these: 1052s 158 (91.86%) aligned 0 times 1052s 6 (3.49%) aligned exactly 1 time 1052s 8 (4.65%) aligned >1 times 1052s 5 (5.49%) were unpaired; of these: 1052s 5 (100.00%) aligned 0 times 1052s 0 (0.00%) aligned exactly 1 time 1052s 0 (0.00%) aligned >1 times 1052s 7.91% overall alignment rate 1052s Read 150 alignments... 1052s Read 200 alignments... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s AAAGA 1052s AAAGA 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s GACGT 1052s GACGT 1052s Processing line... 1052s Processing line... 1052s CCGTATCGC 1052s CCGTATCGC 1052s Processing line... 1052s CCGTATCGC 1052s CCGTATCGC 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s ACG 1052s ACG 1052s Processing line... 1052s ACG 1052s ACG 1052s Processing line... 1052s ACG 1052s ACG 1052s Processing line... 1052s ACG 1052s ACG 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s GACGG 1052s GACGG 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s TC 1052s TC 1052s Processing line... 1052s TC 1052s TC 1052s Processing line... 1052s TC 1052s TC 1052s Processing line... 1052s TC 1052s TC 1052s Processing line... 1052s TC 1052s TC 1052s Processing line... 1052s TC 1052s TC 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s ACAACCGAAAGACGGAC 1052s ACAACCGAAAGACGGAC 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s AGACGGACGT 1052s AGACGGACGT 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s CCGT 1052s CCGT 1052s Processing line... 1052s CCGT 1052s CCGT 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s GTATCG 1052s GTATCG 1052s Processing line... 1052s GTATCG 1052s GTATCG 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s TCC 1052s TCC 1052s Processing line... 1052s TCC 1052s TCC 1052s Processing line... 1052s TCC 1052s TCC 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s CAACCGA 1052s CAACCGA 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s AG 1052s AG 1052s Processing line... 1052s AG 1052s AG 1052s Processing line... 1052s AG 1052s AG 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s TA 1052s TA 1052s Processing line... 1052s TA 1052s TA 1052s Processing line... 1052s TA 1052s TA 1052s Processing line... 1052s TA 1052s TA 1052s Processing line... 1052s TA 1052s TA 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s Processing line... 1052s --- Summary --- 1052s Read 1 reference strings 1052s Checked 33 alignments, 0 edits 1052s --------------- 1052s PASSED 1052s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1052s /usr/bin/bowtie2 --large-index --score-min L,7.82044783175833,9.61442281642274 --trim5 2 -a --mp 3.57372232422531,2.51205956354973 --cp-ival 1 -R 4 --cp-min 4 --np 2 --nofw -q -p 4 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.fastq -2 /tmp/Sim.pm.rtAHg7h8_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1053s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1053s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1053s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 1053s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1053s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1053s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1053s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 1053s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1053s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 1053s Warning: skipping mate #1 of read '54' because it was < 2 characters long 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1053s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 1053s Warning: skipping mate #2 of read '65' because it was < 2 characters long 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1053s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 1053s Warning: skipping mate #2 of read '41' because it was < 2 characters long 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1053s 91 reads; of these: 1053s 86 (94.51%) were paired; of these: 1053s 86 (100.00%) aligned concordantly 0 times 1053s 0 (0.00%) aligned concordantly exactly 1 time 1053s 0 (0.00%) aligned concordantly >1 times 1053s ---- 1053s 86 pairs aligned concordantly 0 times; of these: 1053s 0 (0.00%) aligned discordantly 1 time 1053s ---- 1053s 86 pairs aligned 0 times concordantly or discordantly; of these: 1053s 172 mates make up the pairs; of these: 1053s 158 (91.86%) aligned 0 times 1053s 6 (3.49%) aligned exactly 1 time 1053s 8 (4.65%) aligned >1 times 1053s 5 (5.49%) were unpaired; of these: 1053s 5 (100.00%) aligned 0 times 1053s 0 (0.00%) aligned exactly 1 time 1053s 0 (0.00%) aligned >1 times 1053s 7.91% overall alignment rate 1053s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1053s Flattened IUPAC characters 1053s Mutating sequence Sim.pm.2 1053s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1053s Finished SNPs 1053s Finished ref gaps 1053s Finished read gaps 1053s Mutating sequence Sim.pm.1 1053s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1053s Finished SNPs 1053s Finished ref gaps 1053s Finished read gaps 1053s Mutated reference genome to subject genome 1053s SNPs introduced: 6 1053s Reference gaps introduced: 0 1053s Read gaps introduced: 1 1053s Rearrangements introduced: 2 1053s Created read sampler 1053s Sampling 30 reads 1053s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1053s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1053s parsing sequence Sim.pm.1... 1053s parsing sequence Sim.pm.2... 1053s Parsed 81 reference bases 1053s *** Run 95 of 100 1053s /usr/bin/bowtie2 --large-index --ma 10.476914684073 --score-min L,9.31296399822549,5.97224840225704 --mp 8.26382205375697,5.01611763721798 --trim3 9 --trim5 1 --rfg 9.96868768862377,7.89884811146282 -N 1 -L12 --cp-ival 1 --cp-min 2 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1053s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1053s 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 1053s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 1053s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1053s 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 1053s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 1053s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1053s 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 1053s 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 1053s 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 1053s 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 1053s 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 1053s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 1053s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1053s 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 1053s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 1053s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1053s 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 1053s 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 1053s 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 1053s 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 1053s 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 1053s 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 1053s 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 1053s 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 1053s 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 1053s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (1) 1053s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1053s 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 1053s 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 1053s 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 1053s 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 1053s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (1) 1053s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1053s 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 1053s 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 1053s 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 1053s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (1) 1053s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1053s 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 1053s 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 1053s 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 1053s 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 1053s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (1) 1053s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1053s 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 1053s 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 1053s 30 reads; of these: 1053s 30 (100.00%) were unpaired; of these: 1053s 24 (80.00%) aligned 0 times 1053s 4 (13.33%) aligned exactly 1 time 1053s 2 (6.67%) aligned >1 times 1053s 20.00% overall alignment rate 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s GGAC 1053s GGAC 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s ACAACCGAAAGACG 1053s ACAACCGAAAGACG 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s TG 1053s TG 1053s Processing line... 1053s Processing line... 1053s GTTCA 1053s GTTCA 1053s Processing line... 1053s CAA 1053s CAA 1053s Processing line... 1053s CG 1053s CG 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s --- Summary --- 1053s Read 1 reference strings 1053s Checked 6 alignments, 0 edits 1053s --------------- 1053s PASSED 1053s Flattened IUPAC characters 1053s Mutating sequence Sim.pm.2 1053s Introducing 7 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1053s Finished SNPs 1053s Finished ref gaps 1053s Finished read gaps 1053s Mutating sequence Sim.pm.1 1053s Introducing 4 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1053s Finished SNPs 1053s Finished ref gaps 1053s Finished read gaps 1053s Mutated reference genome to subject genome 1053s SNPs introduced: 11 1053s Reference gaps introduced: 2 1053s Read gaps introduced: 1 1053s Rearrangements introduced: 1 1053s Created read sampler 1053s Sampling 81 reads 1053s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1053s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1053s parsing sequence Sim.pm.1... 1053s parsing sequence Sim.pm.2... 1053s Parsed 81 reference bases 1053s *** Run 96 of 100 1053s /usr/bin/bowtie2 --score-min L,3.57141748097282,7.30042835256849 --rfg 26.9316875618852 -N 0 -L19 --nofw --large-index --ma 27.3208928458746 --rdg 22.8874050650883,9.60976604923146 --mm --cp-ival 1 --cp-min 2 -f -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta 1053s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1053s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 1053s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1053s Read 50 alignments... 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1053s Warning: skipping mate #2 of read '78' because length (1) <= # seed mismatches (0) 1053s Warning: skipping mate #2 of read '78' because it was < 2 characters long 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1053s Read 100 alignments... 1053s 81 reads; of these: 1053s 81 (100.00%) were paired; of these: 1053s 80 (98.77%) aligned concordantly 0 times 1053s 0 (0.00%) aligned concordantly exactly 1 time 1053s 1 (1.23%) aligned concordantly >1 times 1053s ---- 1053s 80 pairs aligned concordantly 0 times; of these: 1053s 0 (0.00%) aligned discordantly 1 time 1053s ---- 1053s 80 pairs aligned 0 times concordantly or discordantly; of these: 1053s 160 mates make up the pairs; of these: 1053s 138 (86.25%) aligned 0 times 1053s 8 (5.00%) aligned exactly 1 time 1053s 14 (8.75%) aligned >1 times 1053s 14.81% overall alignment rate 1053s Read 150 alignments... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s TGT 1053s TGT 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s GATGA 1053s GATGA 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s CGC 1053s CGC 1053s Processing line... 1053s GTA 1053s GTA 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s CTCCTGTTCA 1053s CTCCTGTTCA 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s CA 1053s CA 1053s Processing line... 1053s Processing line... 1053s CCG 1053s CCG 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s TCCCG 1053s TCCCG 1053s Processing line... 1053s Processing line... 1053s TA 1053s TA 1053s Processing line... 1053s Processing line... 1053s TTC 1053s TTC 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s GATGACAACCGAAA 1053s GATGACAACCGAAA 1053s Processing line... 1053s Processing line... 1053s GATGACAACCGAAAG 1053s GATGACAACCGAAAG 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s CCGTATCGCG 1053s CCGTATCGCG 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s CC 1053s CC 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s AT 1053s AT 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s ATCCCGTA 1053s ATCCCGTA 1053s Processing line... 1053s Processing line... 1053s CC 1053s CC 1053s Processing line... 1053s Processing line... 1053s GG 1053s GG 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s TATCGCG 1053s TATCGCG 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s AGAC 1053s AGAC 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s CGTAG 1053s CGTAG 1053s Processing line... 1053s Processing line... 1053s AAGACGG 1053s AAGACGG 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s CT 1053s CT 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s AC 1053s AC 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s /usr/bin/bowtie2 --score-min L,3.57141748097282,7.30042835256849 --rfg 26.9316875618852 -N 0 -L19 --nofw --large-index --ma 27.3208928458746 --rdg 22.8874050650883,9.60976604923146 --mm --cp-ival 1 --cp-min 2 -f -p 2 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.fasta -2 /tmp/Sim.pm.rtAHg7h8_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s Processing line... 1053s --- Summary --- 1053s Read 1 reference strings 1053s Checked 24 alignments, 0 edits 1053s --------------- 1053s PASSED 1053s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1053s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1053s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1054s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 1054s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1054s Warning: skipping mate #2 of read '78' because length (1) <= # seed mismatches (0) 1054s Warning: skipping mate #2 of read '78' because it was < 2 characters long 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1054s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1054s 81 reads; of these: 1054s 81 (100.00%) were paired; of these: 1054s 80 (98.77%) aligned concordantly 0 times 1054s 0 (0.00%) aligned concordantly exactly 1 time 1054s 1 (1.23%) aligned concordantly >1 times 1054s ---- 1054s 80 pairs aligned concordantly 0 times; of these: 1054s 0 (0.00%) aligned discordantly 1 time 1054s ---- 1054s 80 pairs aligned 0 times concordantly or discordantly; of these: 1054s 160 mates make up the pairs; of these: 1054s 138 (86.25%) aligned 0 times 1054s 8 (5.00%) aligned exactly 1 time 1054s 14 (8.75%) aligned >1 times 1054s 14.81% overall alignment rate 1054s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1054s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1054s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1054s Flattened IUPAC characters 1054s Mutating sequence Sim.pm.2 1054s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1054s Finished SNPs 1054s Finished ref gaps 1054s Finished read gaps 1054s Mutating sequence Sim.pm.1 1054s Introducing 13 SNPs, 0/0 ref/read gaps, and 3 rearrangements 1054s Finished SNPs 1054s Finished ref gaps 1054s Finished read gaps 1054s Mutated reference genome to subject genome 1054s SNPs introduced: 13 1054s Reference gaps introduced: 0 1054s Read gaps introduced: 0 1054s Rearrangements introduced: 3 1054s Created read sampler 1054s Sampling 126 reads 1054s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.qseq & /tmp/Sim.pm.rtAHg7h8_2.qseq 1054s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1054s *** Run 97 of 100 1054s /usr/bin/bowtie2 --mm --cp-ival 3 --cp-min 6 --large-index -a --trim3 6 --nofw --gbar 2 --score-min L,5.79673771733544,5.33023997352943 --rfg 7.43454591368158,5.32461669509877 --qseq -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.qseq 1054s parsing sequence Sim.pm.1... 1054s parsing sequence Sim.pm.2... 1054s Parsed 81 reference bases 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1054s 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 1054s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (1) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (1) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1054s 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 1054s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 1054s 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 1054s Read 50 alignments... 1054s Read 100 alignments... 1054s 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 1054s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1054s 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 1054s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 1054s 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 1054s 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 1054s 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 1054s 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 1054s Read 150 alignments... 1054s 126 reads; of these: 1054s 126 (100.00%) were unpaired; of these: 1054s 108 (85.71%) aligned 0 times 1054s 6 (4.76%) aligned exactly 1 time 1054s 12 (9.52%) aligned >1 times 1054s 14.29% overall alignment rate 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s ATC 1054s ATC 1054s Processing line... 1054s ATC 1054s ATC 1054s Processing line... 1054s ATC 1054s ATC 1054s Processing line... 1054s ATC 1054s ATC 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s ATC 1054s ATC 1054s Processing line... 1054s ATC 1054s ATC 1054s Processing line... 1054s ATC 1054s ATC 1054s Processing line... 1054s ATC 1054s ATC 1054s Processing line... 1054s AAC 1054s AAC 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s CC 1054s CC 1054s Processing line... 1054s CC 1054s CC 1054s Processing line... 1054s CC 1054s CC 1054s Processing line... 1054s CC 1054s CC 1054s Processing line... 1054s CC 1054s CC 1054s Processing line... 1054s CC 1054s CC 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s GTATCGCGTA 1054s GTATCGCGTA 1054s Processing line... 1054s GTATCGCGTA 1054s GTATCGCGTA 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CA 1054s CA 1054s Processing line... 1054s CA 1054s CA 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s Processing line... 1054s TCGC 1054s TCGC 1054s Processing line... 1054s TCGC 1054s TCGC 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s CG 1054s CG 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s CAC 1054s CAC 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s TC 1054s TC 1054s Processing line... 1054s TC 1054s TC 1054s Processing line... 1054s TC 1054s TC 1054s Processing line... 1054s TC 1054s TC 1054s Processing line... 1054s TC 1054s TC 1054s Processing line... 1054s TC 1054s TC 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s CTCCT 1054s CTCCT 1054s Processing line... 1054s Processing line... 1054s CGGACG 1054s CGGACG 1054s Processing line... 1054s Processing line... 1054s GCGTAG 1054s GCGTAG 1054s Processing line... 1054s GCGTAG 1054s GCGTAG 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s GG 1054s GG 1054s Processing line... 1054s GG 1054s GG 1054s Processing line... 1054s GG 1054s GG 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s TCACGTG 1054s TCACGTG 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s TCACGTG 1054s TCACGTG 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s --- Summary --- 1054s Read 1 reference strings 1054s Checked 73 alignments, 0 edits 1054s --------------- 1054s PASSED 1054s Flattened IUPAC characters 1054s Mutating sequence Sim.pm.1 1054s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1054s Finished SNPs 1054s Finished ref gaps 1054s Finished read gaps 1054s Mutating sequence Sim.pm.2 1054s Introducing 8 SNPs, 0/2 ref/read gaps, and 1 rearrangements 1054s Finished SNPs 1054s Finished ref gaps 1054s Finished read gaps 1054s Mutated reference genome to subject genome 1054s SNPs introduced: 15 1054s Reference gaps introduced: 0 1054s Read gaps introduced: 2 1054s Rearrangements introduced: 1 1054s Created read sampler 1054s Sampling 143 reads 1054s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.fasta & /tmp/Sim.pm.rtAHg7h8_2.fasta 1054s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1054s parsing sequence Sim.pm.1... 1054s parsing sequence Sim.pm.2... 1054s Parsed 81 reference bases 1054s *** Run 98 of 100 1054s /usr/bin/bowtie2 --score-min L,6.66864602632584,7.80607999186814 --n-ceil 1.22939651086866,0.122984285910458 -i C,0.55229496301388 --rfg 44.1558762962229 --trim5 8 --cp-ival 4 --cp-min 4 -k 5 --large-index --local -f -x /tmp/Sim.pm.rtAHg7h8 /tmp/Sim.pm.rtAHg7h8_1.fasta 1054s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '9' because it was < 2 characters long 1054s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '14' because it was < 2 characters long 1054s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '19' because it was < 2 characters long 1054s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '21' because it was < 2 characters long 1054s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '28' because it was < 2 characters long 1054s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '34' because it was < 2 characters long 1054s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '35' because it was < 2 characters long 1054s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '39' because it was < 2 characters long 1054s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 1054s Warning: skipping read '41' because it was < 2 characters long 1054s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '43' because it was < 2 characters long 1054s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '49' because it was < 2 characters long 1054s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '50' because it was < 2 characters long 1054s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '52' because it was < 2 characters long 1054s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '53' because it was < 2 characters long 1054s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '57' because it was < 2 characters long 1054s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '65' because it was < 2 characters long 1054s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '67' because it was < 2 characters long 1054s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '70' because it was < 2 characters long 1054s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '71' because it was < 2 characters long 1054s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '72' because it was < 2 characters long 1054s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '78' because it was < 2 characters long 1054s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '80' because it was < 2 characters long 1054s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '85' because it was < 2 characters long 1054s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '92' because it was < 2 characters long 1054s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '93' because it was < 2 characters long 1054s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '99' because it was < 2 characters long 1054s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '102' because it was < 2 characters long 1054s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '109' because it was < 2 characters long 1054s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '110' because it was < 2 characters long 1054s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '111' because it was < 2 characters long 1054s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '112' because it was < 2 characters long 1054s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '113' because it was < 2 characters long 1054s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '122' because it was < 2 characters long 1054s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '123' because it was < 2 characters long 1054s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '124' because it was < 2 characters long 1054s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '125' because it was < 2 characters long 1054s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '126' because it was < 2 characters long 1054s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '127' because it was < 2 characters long 1054s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '128' because it was < 2 characters long 1054s Warning: skipping read '130' because length (1) <= # seed mismatches (0) 1054s Warning: skipping read '130' because it was < 2 characters long 1054s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '138' because it was < 2 characters long 1054s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '140' because it was < 2 characters long 1054s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '141' because it was < 2 characters long 1054s Warning: skipping read '142' because length (1) <= # seed mismatches (0) 1054s Warning: skipping read '142' because it was < 2 characters long 1054s 143 reads; of these: 1054s 143 (100.00%) were unpaired; of these: 1054s 143 (100.00%) aligned 0 times 1054s 0 (0.00%) aligned exactly 1 time 1054s 0 (0.00%) aligned >1 times 1054s 0.00% overall alignment rate 1054s Read 50 alignments... 1054s Read 100 alignments... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s /usr/bin/bowtie2 --score-min L,6.66864602632584,7.80607999186814 --n-ceil 1.22939651086866,0.122984285910458 -i C,0.55229496301388 --rfg 44.1558762962229 --trim5 8 --cp-ival 4 --cp-min 4 -k 5 --large-index --local -f -p 4 -x /tmp/Sim.pm.rtAHg7h8 --reorder /tmp/Sim.pm.rtAHg7h8_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s Processing line... 1054s --- Summary --- 1054s Read 1 reference strings 1054s Checked 0 alignments, 0 edits 1054s --------------- 1054s PASSED 1054s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1054s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1054s Warning: skipping read '9' because it was < 2 characters long 1054s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '14' because it was < 2 characters long 1055s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '19' because it was < 2 characters long 1055s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '21' because it was < 2 characters long 1055s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '28' because it was < 2 characters long 1055s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '34' because it was < 2 characters long 1055s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '35' because it was < 2 characters long 1055s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '39' because it was < 2 characters long 1055s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 1055s Warning: skipping read '41' because it was < 2 characters long 1055s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '43' because it was < 2 characters long 1055s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '49' because it was < 2 characters long 1055s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '50' because it was < 2 characters long 1055s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '52' because it was < 2 characters long 1055s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '53' because it was < 2 characters long 1055s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '57' because it was < 2 characters long 1055s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '65' because it was < 2 characters long 1055s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '67' because it was < 2 characters long 1055s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '70' because it was < 2 characters long 1055s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '71' because it was < 2 characters long 1055s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '72' because it was < 2 characters long 1055s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '85' because it was < 2 characters long 1055s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '92' because it was < 2 characters long 1055s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '93' because it was < 2 characters long 1055s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '99' because it was < 2 characters long 1055s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '102' because it was < 2 characters long 1055s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '109' because it was < 2 characters long 1055s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '110' because it was < 2 characters long 1055s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '111' because it was < 2 characters long 1055s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '112' because it was < 2 characters long 1055s Warning: skipping read '130' because length (1) <= # seed mismatches (0) 1055s Warning: skipping read '130' because it was < 2 characters long 1055s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '138' because it was < 2 characters long 1055s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '140' because it was < 2 characters long 1055s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '141' because it was < 2 characters long 1055s Warning: skipping read '142' because length (1) <= # seed mismatches (0) 1055s Warning: skipping read '142' because it was < 2 characters long 1055s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '113' because it was < 2 characters long 1055s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '78' because it was < 2 characters long 1055s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '80' because it was < 2 characters long 1055s Warning: skipping read '122' because it was < 2 characters long 1055s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '123' because it was < 2 characters long 1055s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '124' because it was < 2 characters long 1055s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '125' because it was < 2 characters long 1055s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '126' because it was < 2 characters long 1055s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '127' because it was < 2 characters long 1055s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '128' because it was < 2 characters long 1055s 143 reads; of these: 1055s 143 (100.00%) were unpaired; of these: 1055s 143 (100.00%) aligned 0 times 1055s 0 (0.00%) aligned exactly 1 time 1055s 0 (0.00%) aligned >1 times 1055s 0.00% overall alignment rate 1055s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1055s Flattened IUPAC characters 1055s Mutating sequence Sim.pm.1 1055s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1055s Finished SNPs 1055s Finished ref gaps 1055s Finished read gaps 1055s Mutating sequence Sim.pm.2 1055s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1055s Finished SNPs 1055s Finished ref gaps 1055s Finished read gaps 1055s Mutated reference genome to subject genome 1055s SNPs introduced: 10 1055s Reference gaps introduced: 0 1055s Read gaps introduced: 1 1055s Rearrangements introduced: 0 1055s Created read sampler 1055s Sampling 93 reads 1055s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1055s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1055s parsing sequence Sim.pm.1... 1055s parsing sequence Sim.pm.2... 1055s *** Run 99 of 100 1055s /usr/bin/bowtie2 --norc --score-min L,4.77702522699123,6.14678119145166 --cp-min 6 --mm --cp-ival 1 --local --rdg 44.9192379541394,9.56465104222081 --trim3 7 --mp 8.09370278099772,1.55363022492201 --large-index -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1055s Parsed 81 reference bases 1055s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1055s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '25' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1055s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #2 of read '54' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1055s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 1055s Warning: skipping read '60' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1055s Read 50 alignments... 1055s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '81' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '82' because it was < 2 characters long 1055s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #2 of read '85' because it was < 2 characters long 1055s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #2 of read '87' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1055s Read 100 alignments... 1055s 93 reads; of these: 1055s 77 (82.80%) were paired; of these: 1055s 77 (100.00%) aligned concordantly 0 times 1055s 0 (0.00%) aligned concordantly exactly 1 time 1055s 0 (0.00%) aligned concordantly >1 times 1055s ---- 1055s 77 pairs aligned concordantly 0 times; of these: 1055s 0 (0.00%) aligned discordantly 1 time 1055s ---- 1055s 77 pairs aligned 0 times concordantly or discordantly; of these: 1055s 154 mates make up the pairs; of these: 1055s 154 (100.00%) aligned 0 times 1055s 0 (0.00%) aligned exactly 1 time 1055s 0 (0.00%) aligned >1 times 1055s 16 (17.20%) were unpaired; of these: 1055s 16 (100.00%) aligned 0 times 1055s 0 (0.00%) aligned exactly 1 time 1055s 0 (0.00%) aligned >1 times 1055s 0.00% overall alignment rate 1055s Read 150 alignments... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s Processing line... 1055s --- Summary --- 1055s Read 1 reference strings 1055s Checked 0 alignments, 0 edits 1055s --------------- 1055s PASSED 1055s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1055s /usr/bin/bowtie2 --norc --score-min L,4.77702522699123,6.14678119145166 --cp-min 6 --mm --cp-ival 1 --local --rdg 44.9192379541394,9.56465104222081 --trim3 7 --mp 8.09370278099772,1.55363022492201 --large-index -r -p 4 -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als 1055s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1055s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '25' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '81' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '82' because it was < 2 characters long 1055s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #2 of read '85' because it was < 2 characters long 1055s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #2 of read '87' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1055s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #2 of read '54' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1055s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 1055s Warning: skipping read '60' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1055s 93 reads; of these: 1055s 77 (82.80%) were paired; of these: 1055s 77 (100.00%) aligned concordantly 0 times 1055s 0 (0.00%) aligned concordantly exactly 1 time 1055s 0 (0.00%) aligned concordantly >1 times 1055s ---- 1055s 77 pairs aligned concordantly 0 times; of these: 1055s 0 (0.00%) aligned discordantly 1 time 1055s ---- 1055s 77 pairs aligned 0 times concordantly or discordantly; of these: 1055s 154 mates make up the pairs; of these: 1055s 154 (100.00%) aligned 0 times 1055s 0 (0.00%) aligned exactly 1 time 1055s 0 (0.00%) aligned >1 times 1055s 16 (17.20%) were unpaired; of these: 1055s 16 (100.00%) aligned 0 times 1055s 0 (0.00%) aligned exactly 1 time 1055s 0 (0.00%) aligned >1 times 1055s 0.00% overall alignment rate 1055s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.px.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1055s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.rtAHg7h8.debug.als | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.debug.als.sorted 1055s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als.sorted /tmp/Sim.pm.rtAHg7h8.px.als.sorted 1055s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1055s /usr/bin/bowtie2 --norc --score-min L,4.77702522699123,6.14678119145166 --cp-min 6 --mm --cp-ival 1 --local --rdg 44.9192379541394,9.56465104222081 --trim3 7 --mp 8.09370278099772,1.55363022492201 --large-index -r -p 3 -x /tmp/Sim.pm.rtAHg7h8 --reorder -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw | grep -v '^@PG' > /tmp/Sim.pm.rtAHg7h8.px.reord.als 1055s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1055s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1055s Warning: skipping read '25' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '81' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '82' because it was < 2 characters long 1055s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #2 of read '85' because it was < 2 characters long 1055s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #2 of read '87' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1055s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #2 of read '54' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1055s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 1055s Warning: skipping read '60' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1055s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1055s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1055s 93 reads; of these: 1055s 77 (82.80%) were paired; of these: 1055s 77 (100.00%) aligned concordantly 0 times 1055s 0 (0.00%) aligned concordantly exactly 1 time 1055s 0 (0.00%) aligned concordantly >1 times 1055s ---- 1055s 77 pairs aligned concordantly 0 times; of these: 1055s 0 (0.00%) aligned discordantly 1 time 1055s ---- 1055s 77 pairs aligned 0 times concordantly or discordantly; of these: 1055s 154 mates make up the pairs; of these: 1055s 154 (100.00%) aligned 0 times 1055s 0 (0.00%) aligned exactly 1 time 1055s 0 (0.00%) aligned >1 times 1055s 16 (17.20%) were unpaired; of these: 1055s 16 (100.00%) aligned 0 times 1055s 0 (0.00%) aligned exactly 1 time 1055s 0 (0.00%) aligned >1 times 1055s 0.00% overall alignment rate 1055s diff -uw /tmp/Sim.pm.rtAHg7h8.debug.als /tmp/Sim.pm.rtAHg7h8.px.reord.als 1055s Flattened IUPAC characters 1055s Mutating sequence Sim.pm.2 1055s Introducing 11 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1055s Finished SNPs 1055s Finished ref gaps 1055s Finished read gaps 1055s Mutating sequence Sim.pm.1 1055s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1055s Finished SNPs 1055s Finished ref gaps 1055s Finished read gaps 1055s Mutated reference genome to subject genome 1055s SNPs introduced: 16 1055s Reference gaps introduced: 0 1055s Read gaps introduced: 0 1055s Rearrangements introduced: 0 1055s Created read sampler 1055s Sampling 80 reads 1055s Dumping reads to temporary files /tmp/Sim.pm.rtAHg7h8_1.raw & /tmp/Sim.pm.rtAHg7h8_2.raw 1055s Parsing FASTA file /tmp/Sim.pm.rtAHg7h8.fa... 1055s parsing sequence Sim.pm.1... 1055s parsing sequence Sim.pm.2... 1055s Parsed 81 reference bases 1055s *** Run 100 of 100 1055s /usr/bin/bowtie2 --gbar 10 --score-min L,1.02839271743474,2.30649700530444 --trim5 0 -D 36 --nofw --np 2 --large-index --mp 6.74796981717341,4.55231084485837 --cp-ival 1 --cp-min 2 -r -x /tmp/Sim.pm.rtAHg7h8 -1 /tmp/Sim.pm.rtAHg7h8_1.raw -2 /tmp/Sim.pm.rtAHg7h8_2.raw 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1056s Read 50 alignments... 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1056s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 1056s Warning: skipping mate #1 of read '49' because it was < 2 characters long 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1056s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 1056s Warning: skipping mate #2 of read '51' because it was < 2 characters long 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1056s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 1056s Warning: skipping mate #1 of read '54' because it was < 2 characters long 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1056s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 1056s Warning: skipping mate #2 of read '75' because it was < 2 characters long 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1056s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1056s 80 reads; of these: 1056s 80 (100.00%) were paired; of these: 1056s 80 (100.00%) aligned concordantly 0 times 1056s 0 (0.00%) aligned concordantly exactly 1 time 1056s 0 (0.00%) aligned concordantly >1 times 1056s ---- 1056s 80 pairs aligned concordantly 0 times; of these: 1056s 0 (0.00%) aligned discordantly 1 time 1056s ---- 1056s 80 pairs aligned 0 times concordantly or discordantly; of these: 1056s 160 mates make up the pairs; of these: 1056s 145 (90.62%) aligned 0 times 1056s 6 (3.75%) aligned exactly 1 time 1056s 9 (5.62%) aligned >1 times 1056s 9.38% overall alignment rate 1056s Read 100 alignments... 1056s Read 150 alignments... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s AC 1056s AC 1056s Processing line... 1056s Processing line... 1056s TT 1056s TT 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s ACGGAC 1056s ACGGAC 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s GC 1056s GC 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s ATCG 1056s ATCG 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s CGTAG 1056s CGTAG 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s TATCGCGTA 1056s TATCGCGTA 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s CTGT 1056s CTGT 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s CAACCGAAAGAC 1056s CAACCGAAAGAC 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s CT 1056s CT 1056s Processing line... 1056s Processing line... 1056s CGAAAGACGGACG 1056s CGAAAGACGGACG 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s AACCGAAAGA 1056s AACCGAAAGA 1056s Processing line... 1056s Processing line... 1056s CG 1056s CG 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s TATCGCG 1056s TATCGCG 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s AC 1056s AC 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s Processing line... 1056s --- Summary --- 1056s Read 1 reference strings 1056s Checked 15 alignments, 0 edits 1056s --------------- 1056s PASSED 1056s Created DNA generator 1056s N frac: 0.035 1056s IUPAC frac: 0.002 1056s AT/ACGT frac: 0.428 1056s A/AT frac: 0.629 1056s C/CG frac: 0.345 1056s Generating 2 references 1056s Generated reference 'Sim.pm.1' of untrimmed length 122, trimmed length 7 1056s Generated reference 'Sim.pm.2' of untrimmed length 74, trimmed length 0 1056s Wrote references to /tmp/Sim.pm.dpFRpda2.fa 1056s A: 2 1056s G: 3 1056s N: 1 1056s T: 1 1056s *** TEST CASE *** 1056s Executing: /usr/bin/bowtie2-build --threads 1 /tmp/Sim.pm.dpFRpda2.fa /tmp/Sim.pm.dpFRpda2 1056s Settings: 1056s Output files: "/tmp/Sim.pm.dpFRpda2.*.bt2" 1056s Line rate: 6 (line is 64 bytes) 1056s Lines per side: 1 (side is 64 bytes) 1056s Offset rate: 4 (one in 16) 1056s FTable chars: 10 1056s Strings: unpacked 1056s Max bucket size: default 1056s Max bucket size, sqrt multiplier: default 1056s Max bucket size, len divisor: 4 1056s Difference-cover sample period: 1024 1056s Endianness: little 1056s Actual local endianness: little 1056s Sanity checking: disabled 1056s Assertions: disabled 1056s Random seed: 0 1056s Sizeofs: void*:8, int:4, long:8, size_t:8 1056s Input files DNA, FASTA: 1056s /tmp/Sim.pm.dpFRpda2.fa 1056s Reading reference sizes 1056s Building a SMALL index 1056s Warning: Encountered empty reference sequence 1056s Time reading reference sizes: 00:00:00 1056s Calculating joined length 1056s Writing header 1056s Reserving space for joined string 1056s Joining reference sequences 1056s Time to join reference sequences: 00:00:00 1056s bmax according to bmaxDivN setting: 1 1056s Using parameters --bmax 1 --dcv 1024 1056s Doing ahead-of-time memory usage test 1056s Passed! Constructing with these parameters: --bmax 1 --dcv 1024 1056s Constructing suffix-array element generator 1056s Building DifferenceCoverSample 1056s Building sPrime 1056s Building sPrimeOrder 1056s V-Sorting samples 1056s V-Sorting samples time: 00:00:00 1056s Allocating rank array 1056s Ranking v-sort output 1056s Ranking v-sort output time: 00:00:00 1056s Invoking Larsson-Sadakane on ranks 1056s Invoking Larsson-Sadakane on ranks time: 00:00:00 1056s Sanity-checking and returning 1056s Building samples 1056s Reserving space for 14 sample suffixes 1056s Generating random suffixes 1056s QSorting 14 sample offsets, eliminating duplicates 1056s QSorting sample offsets, eliminating duplicates time: 00:00:00 1056s Multikey QSorting 5 samples 1056s (Using difference cover) 1056s Multikey QSorting samples time: 00:00:00 1056s Calculating bucket sizes 1056s Splitting and merging 1056s Splitting and merging time: 00:00:00 1056s Avg bucket size: 0.75 (target: 1) 1056s Converting suffix-array elements to index image 1056s Allocating ftab, absorbFtab 1056s Entering Ebwt loop 1056s Getting block 1 of 4 1056s Reserving size (2) for bucket 1 1056s Calculating Z arrays for bucket 1 1056s Entering block accumulator loop for bucket 1: 1056s bucket 1: 10% 1056s bucket 1: 20% 1056s bucket 1: 30% 1056s bucket 1: 40% 1056s bucket 1: 50% 1056s bucket 1: 100% 1056s Sorting block of length 1 for bucket 1 1056s (Using difference cover) 1056s Sorting block time: 00:00:00 1056s Returning block of 2 for bucket 1 1056s Getting block 2 of 4 1056s Reserving size (2) for bucket 2 1056s Calculating Z arrays for bucket 2 1056s Entering block accumulator loop for bucket 2: 1056s bucket 2: 10% 1056s bucket 2: 20% 1056s bucket 2: 30% 1056s bucket 2: 40% 1056s bucket 2: 50% 1056s bucket 2: 100% 1056s Sorting block of length 1 for bucket 2 1056s (Using difference cover) 1056s Sorting block time: 00:00:00 1056s Returning block of 2 for bucket 2 1056s Getting block 3 of 4 1056s Reserving size (2) for bucket 3 1056s Calculating Z arrays for bucket 3 1056s Entering block accumulator loop for bucket 3: 1056s bucket 3: 10% 1056s bucket 3: 20% 1056s bucket 3: 30% 1056s bucket 3: 40% 1056s bucket 3: 50% 1056s bucket 3: 100% 1056s Sorting block of length 1 for bucket 3 1056s (Using difference cover) 1056s Sorting block time: 00:00:00 1056s Returning block of 2 for bucket 3 1056s Getting block 4 of 4 1056s Reserving size (2) for bucket 4 1056s Calculating Z arrays for bucket 4 1056s Entering block accumulator loop for bucket 4: 1056s bucket 4: 10% 1056s bucket 4: 20% 1056s bucket 4: 30% 1056s bucket 4: 40% 1056s bucket 4: 50% 1056s bucket 4: 100% 1056s Returning block of 1 for bucket 4 1056s Exited Ebwt loop 1056s fchr[A]: 0 1056s fchr[C]: 2 1056s fchr[G]: 2 1056s fchr[T]: 5 1056s fchr[$]: 6 1056s Exiting Ebwt::buildToDisk() 1056s Returning from initFromVector 1056s Wrote 4194551 bytes to primary EBWT file: /tmp/Sim.pm.dpFRpda2.1.bt2.tmp 1056s Wrote 8 bytes to secondary EBWT file: /tmp/Sim.pm.dpFRpda2.2.bt2.tmp 1056s Re-opening _in1 and _in2 as input streams 1056s Returning from Ebwt constructor 1056s Headers: 1056s len: 6 1056s bwtLen: 7 1056s sz: 2 1056s bwtSz: 2 1056s lineRate: 6 1056s offRate: 4 1056s offMask: 0xfffffff0 1056s ftabChars: 10 1056s eftabLen: 20 1056s eftabSz: 80 1056s ftabLen: 1048577 1056s ftabSz: 4194308 1056s offsLen: 1 1056s offsSz: 4 1056s lineSz: 64 1056s sideSz: 64 1056s sideBwtSz: 48 1056s sideBwtLen: 192 1056s numSides: 1 1056s numLines: 1 1056s ebwtTotLen: 64 1056s ebwtTotSz: 64 1056s color: 0 1056s reverse: 0 1056s Total time for call to driver() for forward index: 00:00:00 1056s Reading reference sizes 1056s Warning: Encountered empty reference sequence 1056s Time reading reference sizes: 00:00:00 1056s Calculating joined length 1056s Writing header 1056s Reserving space for joined string 1056s Joining reference sequences 1056s Time to join reference sequences: 00:00:00 1056s Time to reverse reference sequence: 00:00:00 1056s bmax according to bmaxDivN setting: 1 1056s Using parameters --bmax 1 --dcv 1024 1056s Doing ahead-of-time memory usage test 1056s Passed! Constructing with these parameters: --bmax 1 --dcv 1024 1057s Constructing suffix-array element generator 1057s Building DifferenceCoverSample 1057s Building sPrime 1057s Building sPrimeOrder 1057s V-Sorting samples 1057s V-Sorting samples time: 00:00:00 1057s Allocating rank array 1057s Ranking v-sort output 1057s Ranking v-sort output time: 00:00:00 1057s Invoking Larsson-Sadakane on ranks 1057s Invoking Larsson-Sadakane on ranks time: 00:00:00 1057s Sanity-checking and returning 1057s Building samples 1057s Reserving space for 14 sample suffixes 1057s Generating random suffixes 1057s QSorting 14 sample offsets, eliminating duplicates 1057s QSorting sample offsets, eliminating duplicates time: 00:00:00 1057s Multikey QSorting 5 samples 1057s (Using difference cover) 1057s Multikey QSorting samples time: 00:00:00 1057s Calculating bucket sizes 1057s Splitting and merging 1057s Splitting and merging time: 00:00:00 1057s Avg bucket size: 0.75 (target: 1) 1057s Converting suffix-array elements to index image 1057s Allocating ftab, absorbFtab 1057s Entering Ebwt loop 1057s Getting block 1 of 4 1057s Reserving size (2) for bucket 1 1057s Calculating Z arrays for bucket 1 1057s Entering block accumulator loop for bucket 1: 1057s bucket 1: 10% 1057s bucket 1: 20% 1057s bucket 1: 30% 1057s bucket 1: 40% 1057s bucket 1: 50% 1057s bucket 1: 100% 1057s Sorting block of length 1 for bucket 1 1057s (Using difference cover) 1057s Sorting block time: 00:00:00 1057s Returning block of 2 for bucket 1 1057s Getting block 2 of 4 1057s Reserving size (2) for bucket 2 1057s Calculating Z arrays for bucket 2 1057s Entering block accumulator loop for bucket 2: 1057s bucket 2: 10% 1057s bucket 2: 20% 1057s bucket 2: 30% 1057s bucket 2: 40% 1057s bucket 2: 50% 1057s bucket 2: 100% 1057s Sorting block of length 1 for bucket 2 1057s (Using difference cover) 1057s Sorting block time: 00:00:00 1057s Returning block of 2 for bucket 2 1057s Getting block 3 of 4 1057s Reserving size (2) for bucket 3 1057s Calculating Z arrays for bucket 3 1057s Entering block accumulator loop for bucket 3: 1057s bucket 3: 10% 1057s bucket 3: 20% 1057s bucket 3: 30% 1057s bucket 3: 40% 1057s bucket 3: 50% 1057s bucket 3: 100% 1057s Sorting block of length 1 for bucket 3 1057s (Using difference cover) 1057s Sorting block time: 00:00:00 1057s Returning block of 2 for bucket 3 1057s Getting block 4 of 4 1057s Reserving size (2) for bucket 4 1057s Calculating Z arrays for bucket 4 1057s Entering block accumulator loop for bucket 4: 1057s bucket 4: 10% 1057s bucket 4: 20% 1057s bucket 4: 30% 1057s bucket 4: 40% 1057s bucket 4: 50% 1057s bucket 4: 100% 1057s Returning block of 1 for bucket 4 1057s Exited Ebwt loop 1057s fchr[A]: 0 1057s fchr[C]: 2 1057s fchr[G]: 2 1057s fchr[T]: 5 1057s fchr[$]: 6 1057s Exiting Ebwt::buildToDisk() 1057s Returning from initFromVector 1057s Wrote 4194551 bytes to primary EBWT file: /tmp/Sim.pm.dpFRpda2.rev.1.bt2.tmp 1057s Wrote 8 bytes to secondary EBWT file: /tmp/Sim.pm.dpFRpda2.rev.2.bt2.tmp 1057s Re-opening _in1 and _in2 as input streams 1057s Returning from Ebwt constructor 1057s Headers: 1057s len: 6 1057s bwtLen: 7 1057s sz: 2 1057s bwtSz: 2 1057s lineRate: 6 1057s offRate: 4 1057s offMask: 0xfffffff0 1057s ftabChars: 10 1057s eftabLen: 20 1057s eftabSz: 80 1057s ftabLen: 1048577 1057s ftabSz: 4194308 1057s offsLen: 1 1057s offsSz: 4 1057s lineSz: 64 1057s sideSz: 64 1057s sideBwtSz: 48 1057s sideBwtLen: 192 1057s numSides: 1 1057s numLines: 1 1057s ebwtTotLen: 64 1057s ebwtTotSz: 64 1057s color: 0 1057s reverse: 1 1057s Total time for backward call to driver() for mirror index: 00:00:01 1057s Renaming /tmp/Sim.pm.dpFRpda2.3.bt2.tmp to /tmp/Sim.pm.dpFRpda2.3.bt2 1057s Renaming /tmp/Sim.pm.dpFRpda2.4.bt2.tmp to /tmp/Sim.pm.dpFRpda2.4.bt2 1057s Renaming /tmp/Sim.pm.dpFRpda2.1.bt2.tmp to /tmp/Sim.pm.dpFRpda2.1.bt2 1057s Renaming /tmp/Sim.pm.dpFRpda2.2.bt2.tmp to /tmp/Sim.pm.dpFRpda2.2.bt2 1057s Renaming /tmp/Sim.pm.dpFRpda2.rev.1.bt2.tmp to /tmp/Sim.pm.dpFRpda2.rev.1.bt2 1057s Renaming /tmp/Sim.pm.dpFRpda2.rev.2.bt2.tmp to /tmp/Sim.pm.dpFRpda2.rev.2.bt2 1057s Built nucleotide index '/tmp/Sim.pm.dpFRpda2' 1057s Flattened IUPAC characters 1057s Mutating sequence Sim.pm.2 1057s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1057s Finished SNPs 1057s Finished ref gaps 1057s Finished read gaps 1057s Mutating sequence Sim.pm.1 1057s Introducing 2 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1057s Finished SNPs 1057s Finished ref gaps 1057s Finished read gaps 1057s Mutated reference genome to subject genome 1057s SNPs introduced: 5 1057s Reference gaps introduced: 0 1057s Read gaps introduced: 2 1057s Rearrangements introduced: 0 1057s Created read sampler 1057s Sampling 85 reads 1057s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1057s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1057s parsing sequence Sim.pm.1... 1057s parsing sequence Sim.pm.2... 1057s *** Run 1 of 100 1057s /usr/bin/bowtie2 --score-min L,9.81761532439725,2.77235588461638 -R 2 -D 5 --ma 23.6086368922769 --mp 9.68388123676642,2.1675848962016 --trim3 2 --mm --cp-ival 1 --cp-min 9 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1057s Parsed 7 reference bases 1057s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1057s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1057s Warning: skipping read '2' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1057s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1057s Warning: skipping read '5' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1057s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 1057s Warning: skipping read '6' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1057s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 1057s Warning: skipping read '21' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1057s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1057s Warning: skipping read '62' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1057s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 1057s Warning: skipping read '68' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1057s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1057s Warning: skipping read '72' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1057s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1057s Warning: skipping read '74' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1057s 85 reads; of these: 1057s 85 (100.00%) were unpaired; of these: 1057s 84 (98.82%) aligned 0 times 1057s 1 (1.18%) aligned exactly 1 time 1057s 0 (0.00%) aligned >1 times 1057s 1.18% overall alignment rate 1057s Read 50 alignments... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s /usr/bin/bowtie2 --score-min L,9.81761532439725,2.77235588461638 -R 2 -D 5 --ma 23.6086368922769 --mp 9.68388123676642,2.1675848962016 --trim3 2 --mm --cp-ival 1 --cp-min 9 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s AG 1057s AG 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s Processing line... 1057s --- Summary --- 1057s Read 1 reference strings 1057s Checked 1 alignments, 0 edits 1057s --------------- 1057s PASSED 1057s ALSO checking that bowtie2 and bowtie2-align match up 1057s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1057s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1057s Warning: skipping read '2' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1057s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1057s Warning: skipping read '5' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1057s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 1057s Warning: skipping read '6' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1057s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 1057s Warning: skipping read '21' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1057s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1057s Warning: skipping read '62' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1057s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 1057s Warning: skipping read '68' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1057s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1057s Warning: skipping read '72' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1057s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1057s Warning: skipping read '74' because it was < 2 characters long 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1057s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1057s 85 reads; of these: 1057s 85 (100.00%) were unpaired; of these: 1057s 84 (98.82%) aligned 0 times 1057s 1 (1.18%) aligned exactly 1 time 1057s 0 (0.00%) aligned >1 times 1057s 1.18% overall alignment rate 1057s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1057s Flattened IUPAC characters 1057s Mutating sequence Sim.pm.1 1057s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1057s Finished SNPs 1057s Finished ref gaps 1057s Finished read gaps 1057s Mutating sequence Sim.pm.2 1057s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1057s Finished SNPs 1057s Finished ref gaps 1057s Finished read gaps 1057s Mutated reference genome to subject genome 1057s SNPs introduced: 5 1057s Reference gaps introduced: 0 1057s Read gaps introduced: 0 1057s Rearrangements introduced: 0 1057s Created read sampler 1057s Sampling 92 reads 1057s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1057s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1057s parsing sequence Sim.pm.1... 1057s parsing sequence Sim.pm.2... 1057s Parsed 7 reference bases 1057s *** Run 2 of 100 1057s /usr/bin/bowtie2 --mp 9.64279234113048,4.77518691210583 --rfg 42.3745495871812 --ma 9.33646499486618 --score-min L,4.69680798809448,5.25297906133496 --cp-min 4 --np 2 -N 1 -L21 --cp-ival 2 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1057s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s 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 1057s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (1) 1057s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1058s 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 1058s 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 1058s 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 1058s 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 1058s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s Read 50 alignments... 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s Read 100 alignments... 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 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 1058s 92 reads; of these: 1058s 92 (100.00%) were paired; of these: 1058s 92 (100.00%) aligned concordantly 0 times 1058s 0 (0.00%) aligned concordantly exactly 1 time 1058s 0 (0.00%) aligned concordantly >1 times 1058s ---- 1058s 92 pairs aligned concordantly 0 times; of these: 1058s 0 (0.00%) aligned discordantly 1 time 1058s ---- 1058s 92 pairs aligned 0 times concordantly or discordantly; of these: 1058s 184 mates make up the pairs; of these: 1058s 178 (96.74%) aligned 0 times 1058s 6 (3.26%) aligned exactly 1 time 1058s 0 (0.00%) aligned >1 times 1058s 3.26% overall alignment rate 1058s Read 150 alignments... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s GGT 1058s GGT 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s GA 1058s GA 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s GG 1058s GG 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s GG 1058s GG 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s AG 1058s AG 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s GA 1058s GA 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s --- Summary --- 1058s Read 1 reference strings 1058s Checked 6 alignments, 0 edits 1058s --------------- 1058s PASSED 1058s Flattened IUPAC characters 1058s Mutating sequence Sim.pm.1 1058s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1058s Finished SNPs 1058s Finished ref gaps 1058s Finished read gaps 1058s Mutating sequence Sim.pm.2 1058s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1058s Finished SNPs 1058s Finished ref gaps 1058s Finished read gaps 1058s Mutated reference genome to subject genome 1058s SNPs introduced: 4 1058s Reference gaps introduced: 1 1058s Read gaps introduced: 0 1058s Rearrangements introduced: 0 1058s Created read sampler 1058s Sampling 110 reads 1058s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1058s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1058s parsing sequence Sim.pm.1... 1058s parsing sequence Sim.pm.2... 1058s Parsed 7 reference bases 1058s *** Run 3 of 100 1058s /usr/bin/bowtie2 --np 1 --nofw -N 1 -L19 --rfg 7.38788544059278 --trim5 0 --score-min L,8.83657558733082,7.55889265775023 --cp-min 2 --mm --cp-ival 1 --rdg 48.6064626469972 --trim3 8 --mp 9.84555929148222,7.65121112733751 -M 4 --ma 8.87570380905402 -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw 1058s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1058s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1058s Warning: skipping read '1' because length (1) <= # seed mismatches (1) 1058s Warning: skipping read '1' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1058s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1058s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 1058s Warning: skipping read '18' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1058s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #2 of read '20' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1058s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1058s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1058s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1058s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1058s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1058s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '37' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1058s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1058s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 1058s Warning: skipping read '51' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1058s Warning: skipping read '60' because length (1) <= # seed mismatches (1) 1058s Warning: skipping read '60' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1058s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1058s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '78' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1058s Read 50 alignments... 1058s Read 100 alignments... 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1058s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 1058s Warning: skipping read '82' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1058s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '85' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1058s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '88' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1058s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1058s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '103' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1058s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '108' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1058s 110 reads; of these: 1058s 88 (80.00%) were paired; of these: 1058s 88 (100.00%) aligned concordantly 0 times 1058s 0 (0.00%) aligned concordantly exactly 1 time 1058s 0 (0.00%) aligned concordantly >1 times 1058s ---- 1058s 88 pairs aligned concordantly 0 times; of these: 1058s 0 (0.00%) aligned discordantly 1 time 1058s ---- 1058s 88 pairs aligned 0 times concordantly or discordantly; of these: 1058s 176 mates make up the pairs; of these: 1058s 174 (98.86%) aligned 0 times 1058s 2 (1.14%) aligned exactly 1 time 1058s 0 (0.00%) aligned >1 times 1058s 22 (20.00%) were unpaired; of these: 1058s 22 (100.00%) aligned 0 times 1058s 0 (0.00%) aligned exactly 1 time 1058s 0 (0.00%) aligned >1 times 1058s 1.01% overall alignment rate 1058s Read 150 alignments... 1058s Read 200 alignments... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s GGT 1058s GGT 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s AG 1058s AG 1058s Processing line... 1058s Processing line... 1058s Processing line... 1058s --- Summary --- 1058s Read 1 reference strings 1058s Checked 2 alignments, 0 edits 1058s --------------- 1058s PASSED 1058s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1058s /usr/bin/bowtie2 --np 1 --nofw -N 1 -L19 --rfg 7.38788544059278 --trim5 0 --score-min L,8.83657558733082,7.55889265775023 --cp-min 2 --mm --cp-ival 1 --rdg 48.6064626469972 --trim3 8 --mp 9.84555929148222,7.65121112733751 -M 4 --ma 8.87570380905402 -r -p 3 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1058s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1058s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1058s Warning: skipping read '1' because length (1) <= # seed mismatches (1) 1058s Warning: skipping read '1' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1058s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1058s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 1058s Warning: skipping read '18' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1058s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #2 of read '20' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1058s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (1) 1058s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1058s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 1058s Warning: skipping read '51' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1058s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1058s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1058s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1058s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1058s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1058s Warning: skipping read '60' because length (1) <= # seed mismatches (1) 1058s Warning: skipping read '60' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1058s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 1058s Warning: skipping read '82' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1058s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '85' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1058s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '88' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1058s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '78' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1058s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '103' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1058s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '108' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1058s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '37' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1058s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1058s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (1) 1058s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1058s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1058s 110 reads; of these: 1058s 88 (80.00%) were paired; of these: 1058s 88 (100.00%) aligned concordantly 0 times 1058s 0 (0.00%) aligned concordantly exactly 1 time 1058s 0 (0.00%) aligned concordantly >1 times 1058s ---- 1058s 88 pairs aligned concordantly 0 times; of these: 1058s 0 (0.00%) aligned discordantly 1 time 1058s ---- 1058s 88 pairs aligned 0 times concordantly or discordantly; of these: 1058s 176 mates make up the pairs; of these: 1058s 174 (98.86%) aligned 0 times 1058s 2 (1.14%) aligned exactly 1 time 1058s 0 (0.00%) aligned >1 times 1058s 22 (20.00%) were unpaired; of these: 1058s 22 (100.00%) aligned 0 times 1058s 0 (0.00%) aligned exactly 1 time 1058s 0 (0.00%) aligned >1 times 1058s 1.01% overall alignment rate 1058s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1058s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1058s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1058s Flattened IUPAC characters 1058s Mutating sequence Sim.pm.1 1058s Introducing 10 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1058s Finished SNPs 1058s Finished ref gaps 1058s Finished read gaps 1058s Mutating sequence Sim.pm.2 1058s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1058s Finished SNPs 1058s Finished ref gaps 1058s Finished read gaps 1058s Mutated reference genome to subject genome 1058s SNPs introduced: 13 1058s Reference gaps introduced: 1 1058s Read gaps introduced: 0 1058s Rearrangements introduced: 3 1058s Created read sampler 1058s Sampling 23 reads 1058s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1058s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1058s parsing sequence Sim.pm.1... 1058s parsing sequence Sim.pm.2... 1058s Parsed 7 reference bases 1058s *** Run 4 of 100 1058s /usr/bin/bowtie2 --norc --trim5 0 --score-min L,7.41905346821041,4.6336923846341 --n-ceil 0.201215669560866,1.18793809482583 --cp-min 5 --mm --cp-ival 1 --local --rdg 4.32326841190356,19.2021200848651 --trim3 3 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1059s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1059s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1059s 23 reads; of these: 1059s 20 (86.96%) were paired; of these: 1059s 20 (100.00%) aligned concordantly 0 times 1059s 0 (0.00%) aligned concordantly exactly 1 time 1059s 0 (0.00%) aligned concordantly >1 times 1059s ---- 1059s 20 pairs aligned concordantly 0 times; of these: 1059s 0 (0.00%) aligned discordantly 1 time 1059s ---- 1059s 20 pairs aligned 0 times concordantly or discordantly; of these: 1059s 40 mates make up the pairs; of these: 1059s 40 (100.00%) aligned 0 times 1059s 0 (0.00%) aligned exactly 1 time 1059s 0 (0.00%) aligned >1 times 1059s 3 (13.04%) were unpaired; of these: 1059s 3 (100.00%) aligned 0 times 1059s 0 (0.00%) aligned exactly 1 time 1059s 0 (0.00%) aligned >1 times 1059s 0.00% overall alignment rate 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s --- Summary --- 1059s Read 1 reference strings 1059s Checked 0 alignments, 0 edits 1059s --------------- 1059s PASSED 1059s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1059s /usr/bin/bowtie2 --norc --trim5 0 --score-min L,7.41905346821041,4.6336923846341 --n-ceil 0.201215669560866,1.18793809482583 --cp-min 5 --mm --cp-ival 1 --local --rdg 4.32326841190356,19.2021200848651 --trim3 3 --qseq -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1059s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1059s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1059s 23 reads; of these: 1059s 20 (86.96%) were paired; of these: 1059s 20 (100.00%) aligned concordantly 0 times 1059s 0 (0.00%) aligned concordantly exactly 1 time 1059s 0 (0.00%) aligned concordantly >1 times 1059s ---- 1059s 20 pairs aligned concordantly 0 times; of these: 1059s 0 (0.00%) aligned discordantly 1 time 1059s ---- 1059s 20 pairs aligned 0 times concordantly or discordantly; of these: 1059s 40 mates make up the pairs; of these: 1059s 40 (100.00%) aligned 0 times 1059s 0 (0.00%) aligned exactly 1 time 1059s 0 (0.00%) aligned >1 times 1059s 3 (13.04%) were unpaired; of these: 1059s 3 (100.00%) aligned 0 times 1059s 0 (0.00%) aligned exactly 1 time 1059s 0 (0.00%) aligned >1 times 1059s 0.00% overall alignment rate 1059s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1059s Flattened IUPAC characters 1059s Mutating sequence Sim.pm.2 1059s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1059s Finished SNPs 1059s Finished ref gaps 1059s Finished read gaps 1059s Mutating sequence Sim.pm.1 1059s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1059s Finished SNPs 1059s Finished ref gaps 1059s Finished read gaps 1059s Mutated reference genome to subject genome 1059s SNPs introduced: 5 1059s Reference gaps introduced: 0 1059s Read gaps introduced: 1 1059s Rearrangements introduced: 0 1059s Created read sampler 1059s Sampling 124 reads 1059s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1059s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1059s parsing sequence Sim.pm.1... 1059s parsing sequence Sim.pm.2... 1059s Parsed 7 reference bases 1059s *** Run 5 of 100 1059s /usr/bin/bowtie2 --cp-min 2 --nofw --cp-ival 2 -D 8 --rdg 27.9973987838155 -a -i L,1.41473042045351 --score-min L,4.2995704326143,9.63182842997155 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 1059s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 1059s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (1) <= # seed mismatches (0) 1059s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 1059s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 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 1059s 124 reads; of these: 1059s 124 (100.00%) were unpaired; of these: 1059s 118 (95.16%) aligned 0 times 1059s 6 (4.84%) aligned exactly 1 time 1059s 0 (0.00%) aligned >1 times 1059s 4.84% overall alignment rate 1059s Read 50 alignments... 1059s Read 100 alignments... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s GT 1059s GT 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s GAGG 1059s GAGG 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s GAGG 1059s GAGG 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s AG 1059s AG 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s AG 1059s AG 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s GAGGT 1059s GAGGT 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s --- Summary --- 1059s Read 1 reference strings 1059s Checked 6 alignments, 0 edits 1059s --------------- 1059s PASSED 1059s Flattened IUPAC characters 1059s Mutating sequence Sim.pm.1 1059s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1059s Finished SNPs 1059s Finished ref gaps 1059s Finished read gaps 1059s Mutating sequence Sim.pm.2 1059s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1059s Finished SNPs 1059s Finished ref gaps 1059s Finished read gaps 1059s Mutated reference genome to subject genome 1059s SNPs introduced: 2 1059s Reference gaps introduced: 0 1059s Read gaps introduced: 0 1059s Rearrangements introduced: 0 1059s Created read sampler 1059s Sampling 116 reads 1059s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1059s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1059s parsing sequence Sim.pm.1... 1059s *** Run 6 of 100 1059s /usr/bin/bowtie2 --rdg 4.50639126731235 -a --cp-min 5 --mm --cp-ival 1 --trim5 8 --gbar 2 --score-min L,6.7958443037452,3.40612813342404 --np 8 -D 10 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1059s parsing sequence Sim.pm.2... 1059s Parsed 7 reference bases 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1059s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1059s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1059s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1059s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1059s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read '62' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1059s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1059s Read 50 alignments... 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1059s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read '87' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1059s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1059s Warning: skipping read '93' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1059s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read '98' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1059s Read 100 alignments... 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1059s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read '104' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1059s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 1059s Warning: skipping mate #1 of read '112' because it was < 2 characters long 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1059s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1059s 116 reads; of these: 1059s 95 (81.90%) were paired; of these: 1059s 95 (100.00%) aligned concordantly 0 times 1059s 0 (0.00%) aligned concordantly exactly 1 time 1059s 0 (0.00%) aligned concordantly >1 times 1059s ---- 1059s 95 pairs aligned concordantly 0 times; of these: 1059s 0 (0.00%) aligned discordantly 1 time 1059s ---- 1059s 95 pairs aligned 0 times concordantly or discordantly; of these: 1059s 190 mates make up the pairs; of these: 1059s 187 (98.42%) aligned 0 times 1059s 3 (1.58%) aligned exactly 1 time 1059s 0 (0.00%) aligned >1 times 1059s 21 (18.10%) were unpaired; of these: 1059s 21 (100.00%) aligned 0 times 1059s 0 (0.00%) aligned exactly 1 time 1059s 0 (0.00%) aligned >1 times 1059s 1.42% overall alignment rate 1059s Read 150 alignments... 1059s Read 200 alignments... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s 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Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s GGTA 1059s GGTA 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s AGG 1059s AGG 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s GAGGT 1059s GAGGT 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s Processing line... 1059s --- Summary --- 1059s Read 1 reference strings 1059s Checked 3 alignments, 0 edits 1059s --------------- 1059s PASSED 1059s ALSO checking that bowtie2 and bowtie2-align match up 1059s /usr/bin/bowtie2 --rdg 4.50639126731235 -a --cp-min 5 --mm --cp-ival 1 --trim5 8 --gbar 2 --score-min L,6.7958443037452,3.40612813342404 --np 8 -D 10 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1060s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1060s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1060s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1060s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1060s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1060s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1060s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1060s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1060s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 1060s Warning: skipping mate #1 of read '62' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1060s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 1060s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1060s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 1060s Warning: skipping mate #1 of read '87' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1060s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '93' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1060s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 1060s Warning: skipping mate #1 of read '98' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1060s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 1060s Warning: skipping mate #1 of read '104' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1060s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 1060s Warning: skipping mate #1 of read '112' because it was < 2 characters long 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1060s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1060s 116 reads; of these: 1060s 95 (81.90%) were paired; of these: 1060s 95 (100.00%) aligned concordantly 0 times 1060s 0 (0.00%) aligned concordantly exactly 1 time 1060s 0 (0.00%) aligned concordantly >1 times 1060s ---- 1060s 95 pairs aligned concordantly 0 times; of these: 1060s 0 (0.00%) aligned discordantly 1 time 1060s ---- 1060s 95 pairs aligned 0 times concordantly or discordantly; of these: 1060s 190 mates make up the pairs; of these: 1060s 187 (98.42%) aligned 0 times 1060s 3 (1.58%) aligned exactly 1 time 1060s 0 (0.00%) aligned >1 times 1060s 21 (18.10%) were unpaired; of these: 1060s 21 (100.00%) aligned 0 times 1060s 0 (0.00%) aligned exactly 1 time 1060s 0 (0.00%) aligned >1 times 1060s 1.42% overall alignment rate 1060s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1060s Flattened IUPAC characters 1060s Mutating sequence Sim.pm.2 1060s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1060s Finished SNPs 1060s Finished ref gaps 1060s Finished read gaps 1060s Mutating sequence Sim.pm.1 1060s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1060s Finished SNPs 1060s Finished ref gaps 1060s Finished read gaps 1060s Mutated reference genome to subject genome 1060s SNPs introduced: 5 1060s Reference gaps introduced: 0 1060s Read gaps introduced: 0 1060s Rearrangements introduced: 2 1060s Created read sampler 1060s Sampling 100 reads 1060s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1060s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1060s parsing sequence Sim.pm.1... 1060s parsing sequence Sim.pm.2... 1060s *** Run 7 of 100 1060s /usr/bin/bowtie2 --local --trim3 5 --rdg 44.5757537446632,10.665497402459 --cp-min 6 --cp-ival 1 --mm -i S,2.19664169322445 --score-min L,3.02113808542338,2.73528256616509 --gbar 3 --np 2 --norc -D 35 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1060s Parsed 7 reference bases 1060s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '3' because it was < 2 characters long 1060s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '4' because it was < 2 characters long 1060s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '6' because it was < 2 characters long 1060s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '7' because it was < 2 characters long 1060s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '8' because it was < 2 characters long 1060s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '11' because it was < 2 characters long 1060s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '14' because it was < 2 characters long 1060s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '15' because it was < 2 characters long 1060s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '21' because it was < 2 characters long 1060s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '33' because it was < 2 characters long 1060s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '35' because it was < 2 characters long 1060s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '39' because it was < 2 characters long 1060s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '42' because it was < 2 characters long 1060s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '49' because it was < 2 characters long 1060s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '53' because it was < 2 characters long 1060s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '57' because it was < 2 characters long 1060s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '64' because it was < 2 characters long 1060s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '65' because it was < 2 characters long 1060s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '66' because it was < 2 characters long 1060s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '69' because it was < 2 characters long 1060s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '73' because it was < 2 characters long 1060s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '74' because it was < 2 characters long 1060s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '79' because it was < 2 characters long 1060s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '89' because it was < 2 characters long 1060s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '92' because it was < 2 characters long 1060s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '94' because it was < 2 characters long 1060s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '95' because it was < 2 characters long 1060s 100 reads; of these: 1060s 100 (100.00%) were unpaired; of these: 1060s 100 (100.00%) aligned 0 times 1060s 0 (0.00%) aligned exactly 1 time 1060s 0 (0.00%) aligned >1 times 1060s 0.00% overall alignment rate 1060s Read 50 alignments... 1060s Read 100 alignments... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s Processing line... 1060s --- Summary --- 1060s Read 1 reference strings 1060s Checked 0 alignments, 0 edits 1060s --------------- 1060s PASSED 1060s ALSO checking that bowtie2 and bowtie2-align match up 1060s /usr/bin/bowtie2 --local --trim3 5 --rdg 44.5757537446632,10.665497402459 --cp-min 6 --cp-ival 1 --mm -i S,2.19664169322445 --score-min L,3.02113808542338,2.73528256616509 --gbar 3 --np 2 --norc -D 35 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1060s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '3' because it was < 2 characters long 1060s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '4' because it was < 2 characters long 1060s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '6' because it was < 2 characters long 1060s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '7' because it was < 2 characters long 1060s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '8' because it was < 2 characters long 1060s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '11' because it was < 2 characters long 1060s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '14' because it was < 2 characters long 1060s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '15' because it was < 2 characters long 1060s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '21' because it was < 2 characters long 1060s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '33' because it was < 2 characters long 1060s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '35' because it was < 2 characters long 1060s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '39' because it was < 2 characters long 1060s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '42' because it was < 2 characters long 1060s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '49' because it was < 2 characters long 1060s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '53' because it was < 2 characters long 1060s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '57' because it was < 2 characters long 1060s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '64' because it was < 2 characters long 1060s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '65' because it was < 2 characters long 1060s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '66' because it was < 2 characters long 1060s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '69' because it was < 2 characters long 1060s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '73' because it was < 2 characters long 1060s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '74' because it was < 2 characters long 1060s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '79' because it was < 2 characters long 1060s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '89' because it was < 2 characters long 1060s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '92' because it was < 2 characters long 1060s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '94' because it was < 2 characters long 1060s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '95' because it was < 2 characters long 1060s 100 reads; of these: 1060s 100 (100.00%) were unpaired; of these: 1060s 100 (100.00%) aligned 0 times 1060s 0 (0.00%) aligned exactly 1 time 1060s 0 (0.00%) aligned >1 times 1060s 0.00% overall alignment rate 1060s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1060s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1060s /usr/bin/bowtie2 --local --trim3 5 --rdg 44.5757537446632,10.665497402459 --cp-min 6 --cp-ival 1 --mm -i S,2.19664169322445 --score-min L,3.02113808542338,2.73528256616509 --gbar 3 --np 2 --norc -D 35 -f -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1060s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '3' because it was < 2 characters long 1060s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '4' because it was < 2 characters long 1060s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '6' because it was < 2 characters long 1060s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '7' because it was < 2 characters long 1060s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '8' because it was < 2 characters long 1060s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '11' because it was < 2 characters long 1060s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '14' because it was < 2 characters long 1060s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '15' because it was < 2 characters long 1060s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '21' because it was < 2 characters long 1060s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '33' because it was < 2 characters long 1060s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '35' because it was < 2 characters long 1060s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '39' because it was < 2 characters long 1060s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '42' because it was < 2 characters long 1060s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '49' because it was < 2 characters long 1060s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '65' because it was < 2 characters long 1060s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '66' because it was < 2 characters long 1060s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '69' because it was < 2 characters long 1060s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '73' because it was < 2 characters long 1060s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '74' because it was < 2 characters long 1060s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '79' because it was < 2 characters long 1060s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '89' because it was < 2 characters long 1060s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '92' because it was < 2 characters long 1060s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '94' because it was < 2 characters long 1060s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '95' because it was < 2 characters long 1060s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 1060s Warning: skipping read '53' because it was < 2 characters long 1060s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '57' because it was < 2 characters long 1060s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1060s Warning: skipping read '64' because it was < 2 characters long 1060s 100 reads; of these: 1060s 100 (100.00%) were unpaired; of these: 1060s 100 (100.00%) aligned 0 times 1060s 0 (0.00%) aligned exactly 1 time 1060s 0 (0.00%) aligned >1 times 1060s 0.00% overall alignment rate 1060s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1060s Flattened IUPAC characters 1060s Mutating sequence Sim.pm.2 1060s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1060s Finished SNPs 1060s Finished ref gaps 1060s Finished read gaps 1060s Mutating sequence Sim.pm.1 1060s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1060s Finished SNPs 1060s Finished ref gaps 1060s Finished read gaps 1060s Mutated reference genome to subject genome 1060s SNPs introduced: 1 1060s Reference gaps introduced: 0 1060s Read gaps introduced: 0 1060s Rearrangements introduced: 2 1060s Created read sampler 1060s Sampling 115 reads 1060s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1060s *** Run 8 of 100 1060s /usr/bin/bowtie2 --cp-min 7 --cp-ival 1 --rdg 36.0748432820484,18.32526547911 --ma 4.96534633406179 --norc --nofw -R 2 --rfg 47.7829323390263,19.7779698302631 --score-min L,2.51645104815175,2.02683867992893 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1060s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1060s parsing sequence Sim.pm.1... 1060s parsing sequence Sim.pm.2... 1060s Parsed 7 reference bases 1061s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1061s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 1061s Warning: skipping read '39' because it was < 2 characters long 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1061s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 1061s Warning: skipping read '44' because it was < 2 characters long 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1061s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 1061s Warning: skipping read '102' because it was < 2 characters long 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1061s 115 reads; of these: 1061s 115 (100.00%) were unpaired; of these: 1061s 115 (100.00%) aligned 0 times 1061s 0 (0.00%) aligned exactly 1 time 1061s 0 (0.00%) aligned >1 times 1061s 0.00% overall alignment rate 1061s Read 50 alignments... 1061s Read 100 alignments... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s --- Summary --- 1061s Read 1 reference strings 1061s Checked 0 alignments, 0 edits 1061s --------------- 1061s PASSED 1061s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1061s /usr/bin/bowtie2 --cp-min 7 --cp-ival 1 --rdg 36.0748432820484,18.32526547911 --ma 4.96534633406179 --norc --nofw -R 2 --rfg 47.7829323390263,19.7779698302631 --score-min L,2.51645104815175,2.02683867992893 -r -p 4 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1061s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1061s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 1061s Warning: skipping read '39' because it was < 2 characters long 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1061s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 1061s Warning: skipping read '44' because it was < 2 characters long 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1061s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 1061s Warning: skipping read '102' because it was < 2 characters long 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1061s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1061s 115 reads; of these: 1061s 115 (100.00%) were unpaired; of these: 1061s 115 (100.00%) aligned 0 times 1061s 0 (0.00%) aligned exactly 1 time 1061s 0 (0.00%) aligned >1 times 1061s 0.00% overall alignment rate 1061s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1061s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1061s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1061s Flattened IUPAC characters 1061s Mutating sequence Sim.pm.1 1061s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1061s Finished SNPs 1061s Finished ref gaps 1061s Finished read gaps 1061s Mutating sequence Sim.pm.2 1061s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1061s Finished SNPs 1061s Finished ref gaps 1061s Finished read gaps 1061s Mutated reference genome to subject genome 1061s SNPs introduced: 4 1061s Reference gaps introduced: 0 1061s Read gaps introduced: 1 1061s Rearrangements introduced: 0 1061s Created read sampler 1061s Sampling 54 reads 1061s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1061s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1061s parsing sequence Sim.pm.1... 1061s parsing sequence Sim.pm.2... 1061s Parsed 7 reference bases 1061s *** Run 9 of 100 1061s /usr/bin/bowtie2 --cp-ival 2 --cp-min 2 --trim3 0 --mp 6.77184809167268,6.17664267821919 --local -N 1 -L18 -D 20 --score-min L,3.17865475974309,3.48496937808692 --trim5 8 --rfg 12.3211514061773,8.38145773318778 -i L,0.0171833825114125,1.1891352334416 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1061s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '5' because it was < 2 characters long 1061s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '9' because it was < 2 characters long 1061s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '12' because it was < 2 characters long 1061s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '17' because it was < 2 characters long 1061s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '18' because it was < 2 characters long 1061s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '20' because it was < 2 characters long 1061s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '22' because it was < 2 characters long 1061s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '23' because it was < 2 characters long 1061s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '24' because it was < 2 characters long 1061s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '28' because it was < 2 characters long 1061s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '32' because it was < 2 characters long 1061s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '38' because it was < 2 characters long 1061s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '41' because it was < 2 characters long 1061s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '42' because it was < 2 characters long 1061s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '53' because it was < 2 characters long 1061s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 1061s Warning: skipping read '54' because it was < 2 characters long 1061s 54 reads; of these: 1061s 54 (100.00%) were unpaired; of these: 1061s 54 (100.00%) aligned 0 times 1061s 0 (0.00%) aligned exactly 1 time 1061s 0 (0.00%) aligned >1 times 1061s 0.00% overall alignment rate 1061s Read 50 alignments... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s Processing line... 1061s --- Summary --- 1061s Read 1 reference strings 1061s Checked 0 alignments, 0 edits 1061s --------------- 1061s PASSED 1061s ALSO checking that bowtie2 and bowtie2-align match up 1061s /usr/bin/bowtie2 --cp-ival 2 --cp-min 2 --trim3 0 --mp 6.77184809167268,6.17664267821919 --local -N 1 -L18 -D 20 --score-min L,3.17865475974309,3.48496937808692 --trim5 8 --rfg 12.3211514061773,8.38145773318778 -i L,0.0171833825114125,1.1891352334416 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1062s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '5' because it was < 2 characters long 1062s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '9' because it was < 2 characters long 1062s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '12' because it was < 2 characters long 1062s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '17' because it was < 2 characters long 1062s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '18' because it was < 2 characters long 1062s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '20' because it was < 2 characters long 1062s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '22' because it was < 2 characters long 1062s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '23' because it was < 2 characters long 1062s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '24' because it was < 2 characters long 1062s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '28' because it was < 2 characters long 1062s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '32' because it was < 2 characters long 1062s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '38' because it was < 2 characters long 1062s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '41' because it was < 2 characters long 1062s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '42' because it was < 2 characters long 1062s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '53' because it was < 2 characters long 1062s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 1062s Warning: skipping read '54' because it was < 2 characters long 1062s 54 reads; of these: 1062s 54 (100.00%) were unpaired; of these: 1062s 54 (100.00%) aligned 0 times 1062s 0 (0.00%) aligned exactly 1 time 1062s 0 (0.00%) aligned >1 times 1062s 0.00% overall alignment rate 1062s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1062s Flattened IUPAC characters 1062s Mutating sequence Sim.pm.1 1062s Introducing 2 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1062s Finished SNPs 1062s Finished ref gaps 1062s Finished read gaps 1062s Mutating sequence Sim.pm.2 1062s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1062s Finished SNPs 1062s Finished ref gaps 1062s Finished read gaps 1062s Mutated reference genome to subject genome 1062s SNPs introduced: 2 1062s Reference gaps introduced: 1 1062s Read gaps introduced: 0 1062s Rearrangements introduced: 2 1062s Created read sampler 1062s Sampling 32 reads 1062s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1062s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1062s parsing sequence Sim.pm.1... 1062s parsing sequence Sim.pm.2... 1062s Parsed 7 reference bases 1062s *** Run 10 of 100 1062s /usr/bin/bowtie2 --rdg 45.0529761209632 --trim5 6 --mp 8.71047487826569,6.98105057114237 --n-ceil 1.15394382182752,1.35746504710267 -k 11 --score-min L,3.8689298223979,6.45721430418231 --cp-min 2 --norc --np 2 --mm --cp-ival 2 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1062s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1062s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1062s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1062s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1062s Warning: skipping read '20' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1062s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1062s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1062s 32 reads; of these: 1062s 30 (93.75%) were paired; of these: 1062s 30 (100.00%) aligned concordantly 0 times 1062s 0 (0.00%) aligned concordantly exactly 1 time 1062s 0 (0.00%) aligned concordantly >1 times 1062s ---- 1062s 30 pairs aligned concordantly 0 times; of these: 1062s 0 (0.00%) aligned discordantly 1 time 1062s ---- 1062s 30 pairs aligned 0 times concordantly or discordantly; of these: 1062s 60 mates make up the pairs; of these: 1062s 59 (98.33%) aligned 0 times 1062s 1 (1.67%) aligned exactly 1 time 1062s 0 (0.00%) aligned >1 times 1062s 2 (6.25%) were unpaired; of these: 1062s 2 (100.00%) aligned 0 times 1062s 0 (0.00%) aligned exactly 1 time 1062s 0 (0.00%) aligned >1 times 1062s 1.61% overall alignment rate 1062s Read 50 alignments... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s GG 1062s GG 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s Processing line... 1062s --- Summary --- 1062s Read 1 reference strings 1062s Checked 1 alignments, 0 edits 1062s --------------- 1062s PASSED 1062s ALSO checking that bowtie2 and bowtie2-align match up 1062s /usr/bin/bowtie2 --rdg 45.0529761209632 --trim5 6 --mp 8.71047487826569,6.98105057114237 --n-ceil 1.15394382182752,1.35746504710267 -k 11 --score-min L,3.8689298223979,6.45721430418231 --cp-min 2 --norc --np 2 --mm --cp-ival 2 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1062s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1062s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1062s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1062s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1062s Warning: skipping read '20' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1062s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1062s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1062s 32 reads; of these: 1062s 30 (93.75%) were paired; of these: 1062s 30 (100.00%) aligned concordantly 0 times 1062s 0 (0.00%) aligned concordantly exactly 1 time 1062s 0 (0.00%) aligned concordantly >1 times 1062s ---- 1062s 30 pairs aligned concordantly 0 times; of these: 1062s 0 (0.00%) aligned discordantly 1 time 1062s ---- 1062s 30 pairs aligned 0 times concordantly or discordantly; of these: 1062s 60 mates make up the pairs; of these: 1062s 59 (98.33%) aligned 0 times 1062s 1 (1.67%) aligned exactly 1 time 1062s 0 (0.00%) aligned >1 times 1062s 2 (6.25%) were unpaired; of these: 1062s 2 (100.00%) aligned 0 times 1062s 0 (0.00%) aligned exactly 1 time 1062s 0 (0.00%) aligned >1 times 1062s 1.61% overall alignment rate 1062s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1062s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1062s /usr/bin/bowtie2 --rdg 45.0529761209632 --trim5 6 --mp 8.71047487826569,6.98105057114237 --n-ceil 1.15394382182752,1.35746504710267 -k 11 --score-min L,3.8689298223979,6.45721430418231 --cp-min 2 --norc --np 2 --mm --cp-ival 2 -q -p 4 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1062s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1062s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1062s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1062s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1062s Warning: skipping read '20' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1062s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1062s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 1062s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1062s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1062s 32 reads; of these: 1062s 30 (93.75%) were paired; of these: 1062s 30 (100.00%) aligned concordantly 0 times 1062s 0 (0.00%) aligned concordantly exactly 1 time 1062s 0 (0.00%) aligned concordantly >1 times 1062s ---- 1062s 30 pairs aligned concordantly 0 times; of these: 1062s 0 (0.00%) aligned discordantly 1 time 1062s ---- 1062s 30 pairs aligned 0 times concordantly or discordantly; of these: 1062s 60 mates make up the pairs; of these: 1062s 59 (98.33%) aligned 0 times 1062s 1 (1.67%) aligned exactly 1 time 1062s 0 (0.00%) aligned >1 times 1062s 2 (6.25%) were unpaired; of these: 1062s 2 (100.00%) aligned 0 times 1062s 0 (0.00%) aligned exactly 1 time 1062s 0 (0.00%) aligned >1 times 1062s 1.61% overall alignment rate 1062s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1062s Flattened IUPAC characters 1062s Mutating sequence Sim.pm.1 1062s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1062s Finished SNPs 1062s Finished ref gaps 1062s Finished read gaps 1062s Mutating sequence Sim.pm.2 1062s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1062s Finished SNPs 1062s Finished ref gaps 1062s Finished read gaps 1062s Mutated reference genome to subject genome 1062s SNPs introduced: 2 1062s Reference gaps introduced: 1 1062s Read gaps introduced: 0 1062s Rearrangements introduced: 1 1062s Created read sampler 1062s Sampling 136 reads 1062s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1062s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1062s parsing sequence Sim.pm.1... 1062s parsing sequence Sim.pm.2... 1062s Parsed 7 reference bases 1062s *** Run 11 of 100 1062s /usr/bin/bowtie2 -R 4 --cp-ival 3 -N 1 -L24 --np 1 --cp-min 3 --score-min L,5.90866561245014,8.74517940373172 --local --trim3 5 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1063s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (1) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (1) 1063s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 1063s 136 reads; of these: 1063s 136 (100.00%) were unpaired; of these: 1063s 136 (100.00%) aligned 0 times 1063s 0 (0.00%) aligned exactly 1 time 1063s 0 (0.00%) aligned >1 times 1063s 0.00% overall alignment rate 1063s Read 50 alignments... 1063s Read 100 alignments... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s --- Summary --- 1063s Read 1 reference strings 1063s Checked 0 alignments, 0 edits 1063s --------------- 1063s PASSED 1063s Flattened IUPAC characters 1063s Mutating sequence Sim.pm.2 1063s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1063s Finished SNPs 1063s Finished ref gaps 1063s Finished read gaps 1063s Mutating sequence Sim.pm.1 1063s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1063s Finished SNPs 1063s Finished ref gaps 1063s Finished read gaps 1063s Mutated reference genome to subject genome 1063s SNPs introduced: 3 1063s Reference gaps introduced: 0 1063s Read gaps introduced: 1 1063s Rearrangements introduced: 0 1063s Created read sampler 1063s Sampling 69 reads 1063s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1063s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1063s parsing sequence Sim.pm.1... 1063s parsing sequence Sim.pm.2... 1063s Parsed 7 reference bases 1063s *** Run 12 of 100 1063s /usr/bin/bowtie2 --ma 11.5785196764274 --trim3 6 --mp 4.97535412288508,4.66149314270677 --rdg 14.4294452851186 --cp-ival 1 --cp-min 2 --score-min L,7.52285444151733,9.90910654201827 -i L,0.162492758506855 --rfg 18.3873042403352 --trim5 1 -D 38 --np 1 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1063s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1063s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '3' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1063s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '11' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1063s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '25' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1063s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '29' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1063s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '32' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1063s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '33' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1063s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '36' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1063s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '38' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1063s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '46' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1063s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '48' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1063s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '51' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1063s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '53' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1063s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '54' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1063s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '58' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1063s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '59' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1063s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '60' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1063s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '69' because it was < 2 characters long 1063s 69 reads; of these: 1063s 69 (100.00%) were unpaired; of these: 1063s 66 (95.65%) aligned 0 times 1063s 3 (4.35%) aligned exactly 1 time 1063s 0 (0.00%) aligned >1 times 1063s 4.35% overall alignment rate 1063s Read 50 alignments... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s GG 1063s GG 1063s Processing line... 1063s GG 1063s GG 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s GG 1063s GG 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s --- Summary --- 1063s Read 1 reference strings 1063s Checked 3 alignments, 0 edits 1063s --------------- 1063s PASSED 1063s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1063s /usr/bin/bowtie2 --ma 11.5785196764274 --trim3 6 --mp 4.97535412288508,4.66149314270677 --rdg 14.4294452851186 --cp-ival 1 --cp-min 2 --score-min L,7.52285444151733,9.90910654201827 -i L,0.162492758506855 --rfg 18.3873042403352 --trim5 1 -D 38 --np 1 -f -p 2 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1063s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1063s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '3' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1063s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '11' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1063s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '25' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1063s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '29' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1063s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '32' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1063s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '33' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1063s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '36' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1063s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '38' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1063s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '46' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1063s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '48' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1063s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '51' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1063s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '53' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1063s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '54' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1063s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '58' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1063s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '59' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1063s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '60' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1063s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read '69' because it was < 2 characters long 1063s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1063s 69 reads; of these: 1063s 69 (100.00%) were unpaired; of these: 1063s 66 (95.65%) aligned 0 times 1063s 3 (4.35%) aligned exactly 1 time 1063s 0 (0.00%) aligned >1 times 1063s 4.35% overall alignment rate 1063s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1063s Flattened IUPAC characters 1063s Mutating sequence Sim.pm.1 1063s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1063s Finished SNPs 1063s Finished ref gaps 1063s Finished read gaps 1063s Mutating sequence Sim.pm.2 1063s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1063s Finished SNPs 1063s Finished ref gaps 1063s Finished read gaps 1063s Mutated reference genome to subject genome 1063s SNPs introduced: 0 1063s Reference gaps introduced: 2 1063s Read gaps introduced: 1 1063s Rearrangements introduced: 0 1063s Created read sampler 1063s Sampling 12 reads 1063s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1063s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1063s parsing sequence Sim.pm.1... 1063s parsing sequence Sim.pm.2... 1063s Parsed 7 reference bases 1063s *** Run 13 of 100 1063s /usr/bin/bowtie2 --score-min L,9.20237251380536,6.61112068311556 --trim5 7 -R 2 --np 1 --local --mp 9.05789894886381,2.01466913672484 --trim3 5 --rdg 33.7389954947003 --cp-ival 1 --mm --cp-min 5 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1063s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1063s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1063s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1063s 12 reads; of these: 1063s 12 (100.00%) were unpaired; of these: 1063s 12 (100.00%) aligned 0 times 1063s 0 (0.00%) aligned exactly 1 time 1063s 0 (0.00%) aligned >1 times 1063s 0.00% overall alignment rate 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s Processing line... 1063s --- Summary --- 1063s Read 1 reference strings 1063s Checked 0 alignments, 0 edits 1063s --------------- 1063s PASSED 1063s Flattened IUPAC characters 1063s Mutating sequence Sim.pm.1 1063s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1063s Finished SNPs 1063s Finished ref gaps 1063s Finished read gaps 1063s Mutating sequence Sim.pm.2 1063s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1063s Finished SNPs 1063s Finished ref gaps 1063s Finished read gaps 1063s Mutated reference genome to subject genome 1063s SNPs introduced: 0 1063s Reference gaps introduced: 0 1063s Read gaps introduced: 1 1063s Rearrangements introduced: 0 1063s Created read sampler 1063s Sampling 94 reads 1063s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1063s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1063s parsing sequence Sim.pm.1... 1063s parsing sequence Sim.pm.2... 1063s Parsed 7 reference bases 1063s *** Run 14 of 100 1063s /usr/bin/bowtie2 --np 1 --score-min L,7.06676806121845,5.39113972859777 --gbar 9 --rfg 40.2618190009401,3.8883054659264 --cp-ival 1 --cp-min 10 -k 3 --mp 7.50855774303312,4.79344244228797 --rdg 1.17616886364964 --local -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1064s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read '12' because it was < 2 characters long 1064s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read '29' because it was < 2 characters long 1064s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read '30' because it was < 2 characters long 1064s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read '55' because it was < 2 characters long 1064s Warning: skipping read '91' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read '91' because it was < 2 characters long 1064s 94 reads; of these: 1064s 94 (100.00%) were unpaired; of these: 1064s 94 (100.00%) aligned 0 times 1064s 0 (0.00%) aligned exactly 1 time 1064s 0 (0.00%) aligned >1 times 1064s 0.00% overall alignment rate 1064s Read 50 alignments... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s --- Summary --- 1064s Read 1 reference strings 1064s Checked 0 alignments, 0 edits 1064s --------------- 1064s PASSED 1064s ALSO checking that bowtie2 and bowtie2-align match up 1064s /usr/bin/bowtie2 --np 1 --score-min L,7.06676806121845,5.39113972859777 --gbar 9 --rfg 40.2618190009401,3.8883054659264 --cp-ival 1 --cp-min 10 -k 3 --mp 7.50855774303312,4.79344244228797 --rdg 1.17616886364964 --local -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1064s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read '12' because it was < 2 characters long 1064s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read '29' because it was < 2 characters long 1064s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read '30' because it was < 2 characters long 1064s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read '55' because it was < 2 characters long 1064s Warning: skipping read '91' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read '91' because it was < 2 characters long 1064s 94 reads; of these: 1064s 94 (100.00%) were unpaired; of these: 1064s 94 (100.00%) aligned 0 times 1064s 0 (0.00%) aligned exactly 1 time 1064s 0 (0.00%) aligned >1 times 1064s 0.00% overall alignment rate 1064s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1064s Flattened IUPAC characters 1064s Mutating sequence Sim.pm.2 1064s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1064s Finished SNPs 1064s Finished ref gaps 1064s Finished read gaps 1064s Mutating sequence Sim.pm.1 1064s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1064s Finished SNPs 1064s Finished ref gaps 1064s Finished read gaps 1064s Mutated reference genome to subject genome 1064s SNPs introduced: 10 1064s Reference gaps introduced: 0 1064s Read gaps introduced: 0 1064s Rearrangements introduced: 0 1064s Created read sampler 1064s Sampling 169 reads 1064s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1064s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1064s parsing sequence Sim.pm.1... 1064s parsing sequence Sim.pm.2... 1064s Parsed 7 reference bases 1064s *** Run 15 of 100 1064s /usr/bin/bowtie2 -i L,0.495138698763582 --score-min L,9.64203234555794,3.63898634366404 --np 1 --norc -D 34 --local --mp 3.46673397704605,1.6609741827393 --trim3 7 --cp-min 5 --cp-ival 1 --mm --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1064s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1064s Warning: skipping mate #2 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 1064s Warning: skipping mate #2 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1064s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 1064s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1064s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1064s Read 50 alignments... 1064s Read 100 alignments... 1064s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 1064s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (1) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 1064s Warning: skipping mate #2 of read 'R_1_1_1_121_121_1/1' because length (1) <= # seed mismatches (0) 1064s Warning: skipping mate #2 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 1064s Read 150 alignments... 1064s Warning: skipping read 'R_1_1_1_152_152_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping read 'R_1_1_1_152_152_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_155_155_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_155_155_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_156_156_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_156_156_1/1' because it was < 2 characters long 1064s Warning: skipping mate #1 of read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 1064s Warning: skipping mate #1 of read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 1064s Read 200 alignments... 1064s 169 reads; of these: 1064s 141 (83.43%) were paired; of these: 1064s 141 (100.00%) aligned concordantly 0 times 1064s 0 (0.00%) aligned concordantly exactly 1 time 1064s 0 (0.00%) aligned concordantly >1 times 1064s ---- 1064s 141 pairs aligned concordantly 0 times; of these: 1064s 0 (0.00%) aligned discordantly 1 time 1064s ---- 1064s 141 pairs aligned 0 times concordantly or discordantly; of these: 1064s 282 mates make up the pairs; of these: 1064s 282 (100.00%) aligned 0 times 1064s 0 (0.00%) aligned exactly 1 time 1064s 0 (0.00%) aligned >1 times 1064s 28 (16.57%) were unpaired; of these: 1064s 28 (100.00%) aligned 0 times 1064s 0 (0.00%) aligned exactly 1 time 1064s 0 (0.00%) aligned >1 times 1064s 0.00% overall alignment rate 1064s Read 250 alignments... 1064s Read 300 alignments... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s 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Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s Processing line... 1064s --- Summary --- 1064s Read 1 reference strings 1064s Checked 0 alignments, 0 edits 1064s --------------- 1064s PASSED 1064s ALSO checking that bowtie2 and bowtie2-align match up 1064s /usr/bin/bowtie2 -i L,0.495138698763582 --score-min L,9.64203234555794,3.63898634366404 --np 1 --norc -D 34 --local --mp 3.46673397704605,1.6609741827393 --trim3 7 --cp-min 5 --cp-ival 1 --mm --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1065s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1065s Warning: skipping mate #2 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 1065s Warning: skipping mate #2 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1065s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 1065s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1065s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1065s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (1) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 1065s Warning: skipping mate #2 of read 'R_1_1_1_121_121_1/1' because length (1) <= # seed mismatches (0) 1065s Warning: skipping mate #2 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 1065s Warning: skipping read 'R_1_1_1_152_152_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_152_152_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_155_155_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_155_155_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_156_156_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_156_156_1/1' because it was < 2 characters long 1065s Warning: skipping mate #1 of read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping mate #1 of read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 1065s 169 reads; of these: 1065s 141 (83.43%) were paired; of these: 1065s 141 (100.00%) aligned concordantly 0 times 1065s 0 (0.00%) aligned concordantly exactly 1 time 1065s 0 (0.00%) aligned concordantly >1 times 1065s ---- 1065s 141 pairs aligned concordantly 0 times; of these: 1065s 0 (0.00%) aligned discordantly 1 time 1065s ---- 1065s 141 pairs aligned 0 times concordantly or discordantly; of these: 1065s 282 mates make up the pairs; of these: 1065s 282 (100.00%) aligned 0 times 1065s 0 (0.00%) aligned exactly 1 time 1065s 0 (0.00%) aligned >1 times 1065s 28 (16.57%) were unpaired; of these: 1065s 28 (100.00%) aligned 0 times 1065s 0 (0.00%) aligned exactly 1 time 1065s 0 (0.00%) aligned >1 times 1065s 0.00% overall alignment rate 1065s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1065s Flattened IUPAC characters 1065s Mutating sequence Sim.pm.1 1065s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1065s Finished SNPs 1065s Finished ref gaps 1065s Finished read gaps 1065s Mutating sequence Sim.pm.2 1065s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1065s Finished SNPs 1065s Finished ref gaps 1065s Finished read gaps 1065s Mutated reference genome to subject genome 1065s SNPs introduced: 7 1065s Reference gaps introduced: 0 1065s Read gaps introduced: 0 1065s Rearrangements introduced: 1 1065s Created read sampler 1065s Sampling 19 reads 1065s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1065s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1065s parsing sequence Sim.pm.1... 1065s parsing sequence Sim.pm.2... 1065s *** Run 16 of 100 1065s /usr/bin/bowtie2 --cp-min 9 --cp-ival 1 -a --trim5 7 --rfg 43.4809000430985 --ma 5.25653572930281 --score-min L,4.72580957957255,9.57253106854164 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1065s Parsed 7 reference bases 1065s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1065s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read '0' because it was < 2 characters long 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1065s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read '2' because it was < 2 characters long 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1065s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read '4' because it was < 2 characters long 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1065s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read '5' because it was < 2 characters long 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1065s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read '6' because it was < 2 characters long 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1065s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read '7' because it was < 2 characters long 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1065s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read '8' because it was < 2 characters long 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1065s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read '15' because it was < 2 characters long 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1065s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1065s 19 reads; of these: 1065s 19 (100.00%) were unpaired; of these: 1065s 19 (100.00%) aligned 0 times 1065s 0 (0.00%) aligned exactly 1 time 1065s 0 (0.00%) aligned >1 times 1065s 0.00% overall alignment rate 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s --- Summary --- 1065s Read 1 reference strings 1065s Checked 0 alignments, 0 edits 1065s --------------- 1065s PASSED 1065s Flattened IUPAC characters 1065s Mutating sequence Sim.pm.2 1065s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1065s Finished SNPs 1065s Finished ref gaps 1065s Finished read gaps 1065s Mutating sequence Sim.pm.1 1065s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1065s Finished SNPs 1065s Finished ref gaps 1065s Finished read gaps 1065s Mutated reference genome to subject genome 1065s SNPs introduced: 5 1065s Reference gaps introduced: 0 1065s Read gaps introduced: 2 1065s Rearrangements introduced: 0 1065s Created read sampler 1065s Sampling 75 reads 1065s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1065s *** Run 17 of 100 1065s /usr/bin/bowtie2 --cp-min 5 --norc --np 7 --cp-ival 3 --trim5 9 --rfg 18.5837372860954 --ma 26.2958982056712 --score-min L,4.78392790892808,2.70610827813819 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1065s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1065s parsing sequence Sim.pm.1... 1065s parsing sequence Sim.pm.2... 1065s Parsed 7 reference bases 1065s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 75 reads; of these: 1065s 75 (100.00%) were unpaired; of these: 1065s 75 (100.00%) aligned 0 times 1065s 0 (0.00%) aligned exactly 1 time 1065s 0 (0.00%) aligned >1 times 1065s 0.00% overall alignment rate 1065s Read 50 alignments... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s /usr/bin/bowtie2 --cp-min 5 --norc --np 7 --cp-ival 3 --trim5 9 --rfg 18.5837372860954 --ma 26.2958982056712 --score-min L,4.78392790892808,2.70610827813819 --qseq -p 4 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s Processing line... 1065s --- Summary --- 1065s Read 1 reference strings 1065s Checked 0 alignments, 0 edits 1065s --------------- 1065s PASSED 1065s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1065s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1065s 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 1065s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1065s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1065s 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 1065s 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 1065s 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 1065s 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 1065s 75 reads; of these: 1065s 75 (100.00%) were unpaired; of these: 1065s 75 (100.00%) aligned 0 times 1065s 0 (0.00%) aligned exactly 1 time 1065s 0 (0.00%) aligned >1 times 1065s 0.00% overall alignment rate 1065s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1065s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1065s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1065s Flattened IUPAC characters 1065s Mutating sequence Sim.pm.1 1065s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1065s Finished SNPs 1065s Finished ref gaps 1065s Finished read gaps 1065s Mutating sequence Sim.pm.2 1065s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1065s Finished SNPs 1065s Finished ref gaps 1065s Finished read gaps 1065s Mutated reference genome to subject genome 1065s SNPs introduced: 6 1065s Reference gaps introduced: 0 1065s Read gaps introduced: 0 1065s Rearrangements introduced: 0 1065s Created read sampler 1065s Sampling 122 reads 1065s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1065s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1065s *** Run 18 of 100 1065s /usr/bin/bowtie2 --rdg 33.0454718865757 --trim3 4 --mp 7.80100993769516,4.22279373460331 -k 2 --cp-min 4 --cp-ival 1 --trim5 2 --score-min L,7.05865690577116,4.37391403167634 --norc --nofw -R 1 -N 0 -L27 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1065s parsing sequence Sim.pm.1... 1065s parsing sequence Sim.pm.2... 1065s Parsed 7 reference bases 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (1) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (1) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 122 reads; of these: 1066s 122 (100.00%) were unpaired; of these: 1066s 122 (100.00%) aligned 0 times 1066s 0 (0.00%) aligned exactly 1 time 1066s 0 (0.00%) aligned >1 times 1066s 0.00% overall alignment rate 1066s Read 50 alignments... 1066s Read 100 alignments... 1066s Processing line... 1066s /usr/bin/bowtie2 --rdg 33.0454718865757 --trim3 4 --mp 7.80100993769516,4.22279373460331 -k 2 --cp-min 4 --cp-ival 1 --trim5 2 --score-min L,7.05865690577116,4.37391403167634 --norc --nofw -R 1 -N 0 -L27 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s --- Summary --- 1066s Read 1 reference strings 1066s Checked 0 alignments, 0 edits 1066s --------------- 1066s PASSED 1066s ALSO checking that bowtie2 and bowtie2-align match up 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (1) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (1) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 1066s 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 1066s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 1066s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 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 1066s 122 reads; of these: 1066s 122 (100.00%) were unpaired; of these: 1066s 122 (100.00%) aligned 0 times 1066s 0 (0.00%) aligned exactly 1 time 1066s 0 (0.00%) aligned >1 times 1066s 0.00% overall alignment rate 1066s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1066s Flattened IUPAC characters 1066s Mutating sequence Sim.pm.1 1066s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1066s Finished SNPs 1066s Finished ref gaps 1066s Finished read gaps 1066s Mutating sequence Sim.pm.2 1066s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1066s Finished SNPs 1066s Finished ref gaps 1066s Finished read gaps 1066s Mutated reference genome to subject genome 1066s SNPs introduced: 12 1066s Reference gaps introduced: 1 1066s Read gaps introduced: 1 1066s Rearrangements introduced: 0 1066s Created read sampler 1066s Sampling 54 reads 1066s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1066s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1066s parsing sequence Sim.pm.1... 1066s parsing sequence Sim.pm.2... 1066s Parsed 7 reference bases 1066s *** Run 19 of 100 1066s /usr/bin/bowtie2 --rdg 47.4387853752341 --mp 5.26549877951266,1.21640406427642 --local --mm --cp-ival 1 --cp-min 9 --n-ceil 0.104809601981573,0.628457716162738 --score-min L,1.47672879999594,3.7704314046943 --rfg 33.7949750291057,12.9442543146487 --norc --np 3 -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw 1066s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 1066s Warning: skipping mate #2 of read '5' because it was < 2 characters long 1066s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 1066s Warning: skipping mate #2 of read '28' because it was < 2 characters long 1066s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 1066s Warning: skipping mate #2 of read '31' because it was < 2 characters long 1066s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 1066s Warning: skipping mate #2 of read '50' because it was < 2 characters long 1066s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 1066s Warning: skipping mate #2 of read '52' because it was < 2 characters long 1066s 54 reads; of these: 1066s 54 (100.00%) were paired; of these: 1066s 54 (100.00%) aligned concordantly 0 times 1066s 0 (0.00%) aligned concordantly exactly 1 time 1066s 0 (0.00%) aligned concordantly >1 times 1066s ---- 1066s 54 pairs aligned concordantly 0 times; of these: 1066s 0 (0.00%) aligned discordantly 1 time 1066s ---- 1066s 54 pairs aligned 0 times concordantly or discordantly; of these: 1066s 108 mates make up the pairs; of these: 1066s 108 (100.00%) aligned 0 times 1066s 0 (0.00%) aligned exactly 1 time 1066s 0 (0.00%) aligned >1 times 1066s 0.00% overall alignment rate 1066s Read 50 alignments... 1066s Read 100 alignments... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s Processing line... 1066s --- Summary --- 1066s Read 1 reference strings 1066s Checked 0 alignments, 0 edits 1066s --------------- 1066s PASSED 1066s ALSO checking that bowtie2 and bowtie2-align match up 1066s /usr/bin/bowtie2 --rdg 47.4387853752341 --mp 5.26549877951266,1.21640406427642 --local --mm --cp-ival 1 --cp-min 9 --n-ceil 0.104809601981573,0.628457716162738 --score-min L,1.47672879999594,3.7704314046943 --rfg 33.7949750291057,12.9442543146487 --norc --np 3 -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1067s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read '5' because it was < 2 characters long 1067s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read '28' because it was < 2 characters long 1067s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read '31' because it was < 2 characters long 1067s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read '50' because it was < 2 characters long 1067s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read '52' because it was < 2 characters long 1067s 54 reads; of these: 1067s 54 (100.00%) were paired; of these: 1067s 54 (100.00%) aligned concordantly 0 times 1067s 0 (0.00%) aligned concordantly exactly 1 time 1067s 0 (0.00%) aligned concordantly >1 times 1067s ---- 1067s 54 pairs aligned concordantly 0 times; of these: 1067s 0 (0.00%) aligned discordantly 1 time 1067s ---- 1067s 54 pairs aligned 0 times concordantly or discordantly; of these: 1067s 108 mates make up the pairs; of these: 1067s 108 (100.00%) aligned 0 times 1067s 0 (0.00%) aligned exactly 1 time 1067s 0 (0.00%) aligned >1 times 1067s 0.00% overall alignment rate 1067s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1067s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1067s /usr/bin/bowtie2 --rdg 47.4387853752341 --mp 5.26549877951266,1.21640406427642 --local --mm --cp-ival 1 --cp-min 9 --n-ceil 0.104809601981573,0.628457716162738 --score-min L,1.47672879999594,3.7704314046943 --rfg 33.7949750291057,12.9442543146487 --norc --np 3 -r -p 4 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1067s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read '5' because it was < 2 characters long 1067s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read '28' because it was < 2 characters long 1067s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read '31' because it was < 2 characters long 1067s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read '50' because it was < 2 characters long 1067s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read '52' because it was < 2 characters long 1067s 54 reads; of these: 1067s 54 (100.00%) were paired; of these: 1067s 54 (100.00%) aligned concordantly 0 times 1067s 0 (0.00%) aligned concordantly exactly 1 time 1067s 0 (0.00%) aligned concordantly >1 times 1067s ---- 1067s 54 pairs aligned concordantly 0 times; of these: 1067s 0 (0.00%) aligned discordantly 1 time 1067s ---- 1067s 54 pairs aligned 0 times concordantly or discordantly; of these: 1067s 108 mates make up the pairs; of these: 1067s 108 (100.00%) aligned 0 times 1067s 0 (0.00%) aligned exactly 1 time 1067s 0 (0.00%) aligned >1 times 1067s 0.00% overall alignment rate 1067s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1067s Flattened IUPAC characters 1067s Mutating sequence Sim.pm.2 1067s Introducing 0 SNPs, 2/0 ref/read gaps, and 1 rearrangements 1067s Finished SNPs 1067s Finished ref gaps 1067s Finished read gaps 1067s Mutating sequence Sim.pm.1 1067s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1067s Finished SNPs 1067s Finished ref gaps 1067s Finished read gaps 1067s Mutated reference genome to subject genome 1067s SNPs introduced: 1 1067s Reference gaps introduced: 2 1067s Read gaps introduced: 1 1067s Rearrangements introduced: 1 1067s Created read sampler 1067s Sampling 53 reads 1067s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1067s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1067s parsing sequence Sim.pm.1... 1067s parsing sequence Sim.pm.2... 1067s *** Run 20 of 100 1067s /usr/bin/bowtie2 --score-min L,3.0064208416947,6.96042974741968 --trim5 1 --mp 6.60307062336291,2.75461395976235 --trim3 5 --rfg 43.5171839822832,3.16265169942071 --mm --cp-ival 2 --cp-min 5 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1067s Parsed 7 reference bases 1067s 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 1067s 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 1067s 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 1067s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1067s 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 1067s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 53 reads; of these: 1067s 53 (100.00%) were unpaired; of these: 1067s 52 (98.11%) aligned 0 times 1067s 1 (1.89%) aligned exactly 1 time 1067s 0 (0.00%) aligned >1 times 1067s 1.89% overall alignment rate 1067s Read 50 alignments... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s AG 1067s AG 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s --- Summary --- 1067s Read 1 reference strings 1067s Checked 1 alignments, 0 edits 1067s --------------- 1067s PASSED 1067s Flattened IUPAC characters 1067s Mutating sequence Sim.pm.1 1067s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1067s Finished SNPs 1067s Finished ref gaps 1067s Finished read gaps 1067s Mutating sequence Sim.pm.2 1067s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1067s Finished SNPs 1067s Finished ref gaps 1067s Finished read gaps 1067s Mutated reference genome to subject genome 1067s SNPs introduced: 4 1067s Reference gaps introduced: 0 1067s Read gaps introduced: 1 1067s Rearrangements introduced: 0 1067s Created read sampler 1067s Sampling 94 reads 1067s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1067s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1067s parsing sequence Sim.pm.1... 1067s parsing sequence Sim.pm.2... 1067s Parsed 7 reference bases 1067s *** Run 21 of 100 1067s /usr/bin/bowtie2 --cp-min 8 --nofw --cp-ival 3 --mm --mp 8.82421504150065,3.86941888132161 --trim5 5 --rfg 39.1597843885337 --ma 17.3648431771489 --score-min L,7.83479345122233,1.51181007106968 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1067s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 1067s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1067s 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 1067s 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 1067s 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 1067s 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 1067s 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 1067s Read 50 alignments... 1067s 94 reads; of these: 1067s 82 (87.23%) were paired; of these: 1067s 82 (100.00%) aligned concordantly 0 times 1067s 0 (0.00%) aligned concordantly exactly 1 time 1067s 0 (0.00%) aligned concordantly >1 times 1067s ---- 1067s 82 pairs aligned concordantly 0 times; of these: 1067s 0 (0.00%) aligned discordantly 1 time 1067s ---- 1067s 82 pairs aligned 0 times concordantly or discordantly; of these: 1067s 164 mates make up the pairs; of these: 1067s 158 (96.34%) aligned 0 times 1067s 6 (3.66%) aligned exactly 1 time 1067s 0 (0.00%) aligned >1 times 1067s 12 (12.77%) were unpaired; of these: 1067s 12 (100.00%) aligned 0 times 1067s 0 (0.00%) aligned exactly 1 time 1067s 0 (0.00%) aligned >1 times 1067s 3.41% overall alignment rate 1067s Read 100 alignments... 1067s Read 150 alignments... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s GG 1067s GG 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s GA 1067s GA 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s GT 1067s GT 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s GA 1067s GA 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s GT 1067s GT 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s TA 1067s TA 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s /usr/bin/bowtie2 --cp-min 8 --nofw --cp-ival 3 --mm --mp 8.82421504150065,3.86941888132161 --trim5 5 --rfg 39.1597843885337 --ma 17.3648431771489 --score-min L,7.83479345122233,1.51181007106968 --qseq -p 4 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s Processing line... 1067s --- Summary --- 1067s Read 1 reference strings 1067s Checked 6 alignments, 0 edits 1067s --------------- 1067s PASSED 1067s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1068s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 1068s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 94 reads; of these: 1068s 82 (87.23%) were paired; of these: 1068s 82 (100.00%) aligned concordantly 0 times 1068s 0 (0.00%) aligned concordantly exactly 1 time 1068s 0 (0.00%) aligned concordantly >1 times 1068s ---- 1068s 82 pairs aligned concordantly 0 times; of these: 1068s 0 (0.00%) aligned discordantly 1 time 1068s ---- 1068s 82 pairs aligned 0 times concordantly or discordantly; of these: 1068s 164 mates make up the pairs; of these: 1068s 158 (96.34%) aligned 0 times 1068s 6 (3.66%) aligned exactly 1 time 1068s 0 (0.00%) aligned >1 times 1068s 12 (12.77%) were unpaired; of these: 1068s 12 (100.00%) aligned 0 times 1068s 0 (0.00%) aligned exactly 1 time 1068s 0 (0.00%) aligned >1 times 1068s 3.41% overall alignment rate 1068s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1068s Flattened IUPAC characters 1068s Mutating sequence Sim.pm.2 1068s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1068s Finished SNPs 1068s Finished ref gaps 1068s Finished read gaps 1068s Mutating sequence Sim.pm.1 1068s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1068s Finished SNPs 1068s Finished ref gaps 1068s Finished read gaps 1068s Mutated reference genome to subject genome 1068s SNPs introduced: 5 1068s Reference gaps introduced: 0 1068s Read gaps introduced: 1 1068s Rearrangements introduced: 0 1068s Created read sampler 1068s Sampling 28 reads 1068s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1068s *** Run 22 of 100 1068s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 3 --score-min L,3.63329863121285,5.22836097488677 --trim3 5 --mp 2.97780227387007,1.28082945750584 --rdg 28.9610645057124 --trim5 5 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1068s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1068s parsing sequence Sim.pm.1... 1068s parsing sequence Sim.pm.2... 1068s Parsed 7 reference bases 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1068s 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 1068s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1068s 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 1068s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1068s 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 1068s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1068s 28 reads; of these: 1068s 28 (100.00%) were unpaired; of these: 1068s 27 (96.43%) aligned 0 times 1068s 1 (3.57%) aligned exactly 1 time 1068s 0 (0.00%) aligned >1 times 1068s 3.57% overall alignment rate 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s GT 1068s GT 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s --- Summary --- 1068s Read 1 reference strings 1068s Checked 1 alignments, 0 edits 1068s --------------- 1068s PASSED 1068s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1068s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 3 --score-min L,3.63329863121285,5.22836097488677 --trim3 5 --mp 2.97780227387007,1.28082945750584 --rdg 28.9610645057124 --trim5 5 --qseq -p 3 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1068s 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 1068s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1068s 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 1068s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1068s 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 1068s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s 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 1068s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1068s 28 reads; of these: 1068s 28 (100.00%) were unpaired; of these: 1068s 27 (96.43%) aligned 0 times 1068s 1 (3.57%) aligned exactly 1 time 1068s 0 (0.00%) aligned >1 times 1068s 3.57% overall alignment rate 1068s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1068s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1068s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1068s Flattened IUPAC characters 1068s Mutating sequence Sim.pm.2 1068s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1068s Finished SNPs 1068s Finished ref gaps 1068s Finished read gaps 1068s Mutating sequence Sim.pm.1 1068s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1068s Finished SNPs 1068s Finished ref gaps 1068s Finished read gaps 1068s Mutated reference genome to subject genome 1068s SNPs introduced: 1 1068s Reference gaps introduced: 0 1068s Read gaps introduced: 1 1068s Rearrangements introduced: 0 1068s Created read sampler 1068s Sampling 45 reads 1068s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1068s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1068s parsing sequence Sim.pm.1... 1068s parsing sequence Sim.pm.2... 1068s Parsed 7 reference bases 1068s *** Run 23 of 100 1068s /usr/bin/bowtie2 -N 0 -L12 --nofw --score-min L,5.42487306385963,7.3937213776942 --trim5 9 --rfg 44.2940336465802 --cp-ival 1 --mm --cp-min 8 --trim3 2 --mp 9.81426874464976,7.26499091346014 -a --local -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1068s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1068s Warning: skipping read '2' because it was < 2 characters long 1068s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '6' because it was < 2 characters long 1068s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '7' because it was < 2 characters long 1068s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '8' because it was < 2 characters long 1068s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '13' because it was < 2 characters long 1068s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '18' because it was < 2 characters long 1068s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '28' because it was < 2 characters long 1068s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '29' because it was < 2 characters long 1068s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '31' because it was < 2 characters long 1068s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '37' because it was < 2 characters long 1068s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '38' because it was < 2 characters long 1068s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '39' because it was < 2 characters long 1068s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 1068s Warning: skipping read '40' because it was < 2 characters long 1068s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '41' because it was < 2 characters long 1068s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '42' because it was < 2 characters long 1068s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1068s Warning: skipping read '43' because it was < 2 characters long 1068s 45 reads; of these: 1068s 45 (100.00%) were unpaired; of these: 1068s 45 (100.00%) aligned 0 times 1068s 0 (0.00%) aligned exactly 1 time 1068s 0 (0.00%) aligned >1 times 1068s 0.00% overall alignment rate 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s Processing line... 1068s --- Summary --- 1068s Read 1 reference strings 1068s Checked 0 alignments, 0 edits 1068s --------------- 1068s PASSED 1068s ALSO checking that bowtie2 and bowtie2-align match up 1068s /usr/bin/bowtie2 -N 0 -L12 --nofw --score-min L,5.42487306385963,7.3937213776942 --trim5 9 --rfg 44.2940336465802 --cp-ival 1 --mm --cp-min 8 --trim3 2 --mp 9.81426874464976,7.26499091346014 -a --local -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1069s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1069s Warning: skipping read '2' because it was < 2 characters long 1069s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '6' because it was < 2 characters long 1069s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '7' because it was < 2 characters long 1069s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '8' because it was < 2 characters long 1069s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '13' because it was < 2 characters long 1069s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '18' because it was < 2 characters long 1069s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '28' because it was < 2 characters long 1069s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '29' because it was < 2 characters long 1069s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '31' because it was < 2 characters long 1069s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '37' because it was < 2 characters long 1069s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '38' because it was < 2 characters long 1069s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '39' because it was < 2 characters long 1069s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 1069s Warning: skipping read '40' because it was < 2 characters long 1069s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '41' because it was < 2 characters long 1069s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '42' because it was < 2 characters long 1069s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '43' because it was < 2 characters long 1069s 45 reads; of these: 1069s 45 (100.00%) were unpaired; of these: 1069s 45 (100.00%) aligned 0 times 1069s 0 (0.00%) aligned exactly 1 time 1069s 0 (0.00%) aligned >1 times 1069s 0.00% overall alignment rate 1069s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1069s Flattened IUPAC characters 1069s Mutating sequence Sim.pm.1 1069s Introducing 8 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1069s Finished SNPs 1069s Finished ref gaps 1069s Finished read gaps 1069s Mutating sequence Sim.pm.2 1069s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1069s Finished SNPs 1069s Finished ref gaps 1069s Finished read gaps 1069s Mutated reference genome to subject genome 1069s SNPs introduced: 8 1069s Reference gaps introduced: 1 1069s Read gaps introduced: 0 1069s Rearrangements introduced: 1 1069s Created read sampler 1069s Sampling 41 reads 1069s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1069s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1069s parsing sequence Sim.pm.1... 1069s parsing sequence Sim.pm.2... 1069s Parsed 7 reference bases 1069s *** Run 24 of 100 1069s /usr/bin/bowtie2 -i C,4.09190716120047 --score-min L,8.96401137436785,9.63576318465167 --n-ceil 0.957575617308695,0.214718231582572 -D 49 --local --mp 5.93017055097246,5.06851442475977 --trim3 8 --rdg 17.8636956561423,10.8835066105696 --cp-min 5 --cp-ival 3 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1069s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1069s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1069s Warning: skipping mate #2 of read '2' because it was < 2 characters long 1069s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1069s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1069s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1069s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '21' because it was < 2 characters long 1069s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1069s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 1069s Warning: skipping mate #2 of read '23' because it was < 2 characters long 1069s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1069s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '41' because it was < 2 characters long 1069s 41 reads; of these: 1069s 37 (90.24%) were paired; of these: 1069s 37 (100.00%) aligned concordantly 0 times 1069s 0 (0.00%) aligned concordantly exactly 1 time 1069s 0 (0.00%) aligned concordantly >1 times 1069s ---- 1069s 37 pairs aligned concordantly 0 times; of these: 1069s 0 (0.00%) aligned discordantly 1 time 1069s ---- 1069s 37 pairs aligned 0 times concordantly or discordantly; of these: 1069s 74 mates make up the pairs; of these: 1069s 74 (100.00%) aligned 0 times 1069s 0 (0.00%) aligned exactly 1 time 1069s 0 (0.00%) aligned >1 times 1069s 4 (9.76%) were unpaired; of these: 1069s 4 (100.00%) aligned 0 times 1069s 0 (0.00%) aligned exactly 1 time 1069s 0 (0.00%) aligned >1 times 1069s 0.00% overall alignment rate 1069s Read 50 alignments... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s Processing line... 1069s --- Summary --- 1069s Read 1 reference strings 1069s Checked 0 alignments, 0 edits 1069s --------------- 1069s PASSED 1069s ALSO checking that bowtie2 and bowtie2-align match up 1069s /usr/bin/bowtie2 -i C,4.09190716120047 --score-min L,8.96401137436785,9.63576318465167 --n-ceil 0.957575617308695,0.214718231582572 -D 49 --local --mp 5.93017055097246,5.06851442475977 --trim3 8 --rdg 17.8636956561423,10.8835066105696 --cp-min 5 --cp-ival 3 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1069s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1069s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1069s Warning: skipping mate #2 of read '2' because it was < 2 characters long 1069s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1069s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1069s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1069s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '21' because it was < 2 characters long 1069s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1069s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 1069s Warning: skipping mate #2 of read '23' because it was < 2 characters long 1069s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 1069s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1069s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1069s Warning: skipping read '41' because it was < 2 characters long 1069s 41 reads; of these: 1069s 37 (90.24%) were paired; of these: 1069s 37 (100.00%) aligned concordantly 0 times 1069s 0 (0.00%) aligned concordantly exactly 1 time 1069s 0 (0.00%) aligned concordantly >1 times 1069s ---- 1069s 37 pairs aligned concordantly 0 times; of these: 1069s 0 (0.00%) aligned discordantly 1 time 1069s ---- 1069s 37 pairs aligned 0 times concordantly or discordantly; of these: 1069s 74 mates make up the pairs; of these: 1069s 74 (100.00%) aligned 0 times 1069s 0 (0.00%) aligned exactly 1 time 1069s 0 (0.00%) aligned >1 times 1069s 4 (9.76%) were unpaired; of these: 1069s 4 (100.00%) aligned 0 times 1069s 0 (0.00%) aligned exactly 1 time 1069s 0 (0.00%) aligned >1 times 1069s 0.00% overall alignment rate 1069s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1069s Flattened IUPAC characters 1069s Mutating sequence Sim.pm.2 1069s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1069s Finished SNPs 1069s Finished ref gaps 1069s Finished read gaps 1069s Mutating sequence Sim.pm.1 1069s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1069s Finished SNPs 1069s Finished ref gaps 1069s Finished read gaps 1069s Mutated reference genome to subject genome 1069s SNPs introduced: 3 1069s Reference gaps introduced: 1 1069s Read gaps introduced: 0 1069s Rearrangements introduced: 0 1069s Created read sampler 1069s Sampling 91 reads 1069s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1070s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1070s parsing sequence Sim.pm.1... 1070s parsing sequence Sim.pm.2... 1070s Parsed 7 reference bases 1070s *** Run 25 of 100 1070s /usr/bin/bowtie2 --score-min L,6.3635135748883,4.14302310028903 -N 0 -L16 --np 5 --ma 4.5511902779579 --mp 2.31432294553027,1.73997130985258 -a --rdg 17.3836396548941,14.2805038326619 --cp-ival 1 --mm --cp-min 6 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1070s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1070s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1070s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1070s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '50' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1070s Read 50 alignments... 1070s Read 100 alignments... 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1070s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '76' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1070s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '90' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1070s 91 reads; of these: 1070s 91 (100.00%) were paired; of these: 1070s 91 (100.00%) aligned concordantly 0 times 1070s 0 (0.00%) aligned concordantly exactly 1 time 1070s 0 (0.00%) aligned concordantly >1 times 1070s ---- 1070s 91 pairs aligned concordantly 0 times; of these: 1070s 0 (0.00%) aligned discordantly 1 time 1070s ---- 1070s 91 pairs aligned 0 times concordantly or discordantly; of these: 1070s 182 mates make up the pairs; of these: 1070s 180 (98.90%) aligned 0 times 1070s 2 (1.10%) aligned exactly 1 time 1070s 0 (0.00%) aligned >1 times 1070s 1.10% overall alignment rate 1070s Read 150 alignments... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s GAG 1070s GAG 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s GT 1070s GT 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s --- Summary --- 1070s Read 1 reference strings 1070s Checked 2 alignments, 0 edits 1070s --------------- 1070s PASSED 1070s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1070s /usr/bin/bowtie2 --score-min L,6.3635135748883,4.14302310028903 -N 0 -L16 --np 5 --ma 4.5511902779579 --mp 2.31432294553027,1.73997130985258 -a --rdg 17.3836396548941,14.2805038326619 --cp-ival 1 --mm --cp-min 6 -f -p 3 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1070s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1070s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1070s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '50' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1070s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1070s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '90' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1070s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '76' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1070s 91 reads; of these: 1070s 91 (100.00%) were paired; of these: 1070s 91 (100.00%) aligned concordantly 0 times 1070s 0 (0.00%) aligned concordantly exactly 1 time 1070s 0 (0.00%) aligned concordantly >1 times 1070s ---- 1070s 91 pairs aligned concordantly 0 times; of these: 1070s 0 (0.00%) aligned discordantly 1 time 1070s ---- 1070s 91 pairs aligned 0 times concordantly or discordantly; of these: 1070s 182 mates make up the pairs; of these: 1070s 180 (98.90%) aligned 0 times 1070s 2 (1.10%) aligned exactly 1 time 1070s 0 (0.00%) aligned >1 times 1070s 1.10% overall alignment rate 1070s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1070s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1070s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1070s Flattened IUPAC characters 1070s Mutating sequence Sim.pm.2 1070s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1070s Finished SNPs 1070s Finished ref gaps 1070s Finished read gaps 1070s Mutating sequence Sim.pm.1 1070s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1070s Finished SNPs 1070s Finished ref gaps 1070s Finished read gaps 1070s Mutated reference genome to subject genome 1070s SNPs introduced: 1 1070s Reference gaps introduced: 0 1070s Read gaps introduced: 0 1070s Rearrangements introduced: 1 1070s Created read sampler 1070s Sampling 80 reads 1070s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1070s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1070s parsing sequence Sim.pm.1... 1070s parsing sequence Sim.pm.2... 1070s Parsed 7 reference bases 1070s *** Run 26 of 100 1070s /usr/bin/bowtie2 -R 3 --nofw --np 8 --score-min L,4.68070609581658,6.85649292441174 --n-ceil 1.02127584037764,0.964189967352966 -i C,3.21967839434401,7.28807004144693 --rfg 2.61492551968837 --mm --cp-ival 3 --cp-min 6 --ma 12.6330061879966 -a -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1070s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1070s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1070s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1070s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '61' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1070s 80 reads; of these: 1070s 80 (100.00%) were paired; of these: 1070s 80 (100.00%) aligned concordantly 0 times 1070s 0 (0.00%) aligned concordantly exactly 1 time 1070s 0 (0.00%) aligned concordantly >1 times 1070s ---- 1070s 80 pairs aligned concordantly 0 times; of these: 1070s 0 (0.00%) aligned discordantly 1 time 1070s ---- 1070s 80 pairs aligned 0 times concordantly or discordantly; of these: 1070s 160 mates make up the pairs; of these: 1070s 158 (98.75%) aligned 0 times 1070s 2 (1.25%) aligned exactly 1 time 1070s 0 (0.00%) aligned >1 times 1070s 1.25% overall alignment rate 1070s Read 50 alignments... 1070s Read 100 alignments... 1070s Read 150 alignments... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s GAG 1070s GAG 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s GT 1070s GT 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 1070s Processing line... 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1070s Processing line... 1070s Processing line... 1070s --- Summary --- 1070s Read 1 reference strings 1070s Checked 2 alignments, 0 edits 1070s --------------- 1070s PASSED 1070s ALSO checking that bowtie2 and bowtie2-align match up 1070s /usr/bin/bowtie2 -R 3 --nofw --np 8 --score-min L,4.68070609581658,6.85649292441174 --n-ceil 1.02127584037764,0.964189967352966 -i C,3.21967839434401,7.28807004144693 --rfg 2.61492551968837 --mm --cp-ival 3 --cp-min 6 --ma 12.6330061879966 -a -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1070s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1070s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1070s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1070s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 1070s Warning: skipping mate #2 of read '61' because it was < 2 characters long 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1070s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1070s 80 reads; of these: 1070s 80 (100.00%) were paired; of these: 1070s 80 (100.00%) aligned concordantly 0 times 1070s 0 (0.00%) aligned concordantly exactly 1 time 1070s 0 (0.00%) aligned concordantly >1 times 1070s ---- 1070s 80 pairs aligned concordantly 0 times; of these: 1070s 0 (0.00%) aligned discordantly 1 time 1070s ---- 1070s 80 pairs aligned 0 times concordantly or discordantly; of these: 1070s 160 mates make up the pairs; of these: 1070s 158 (98.75%) aligned 0 times 1070s 2 (1.25%) aligned exactly 1 time 1070s 0 (0.00%) aligned >1 times 1070s 1.25% overall alignment rate 1071s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1071s Flattened IUPAC characters 1071s Mutating sequence Sim.pm.2 1071s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1071s Finished SNPs 1071s Finished ref gaps 1071s Finished read gaps 1071s Mutating sequence Sim.pm.1 1071s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1071s Finished SNPs 1071s Finished ref gaps 1071s Finished read gaps 1071s Mutated reference genome to subject genome 1071s SNPs introduced: 8 1071s Reference gaps introduced: 1 1071s Read gaps introduced: 0 1071s Rearrangements introduced: 0 1071s Created read sampler 1071s Sampling 93 reads 1071s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1071s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1071s parsing sequence Sim.pm.1... 1071s parsing sequence Sim.pm.2... 1071s Parsed 7 reference bases 1071s *** Run 27 of 100 1071s /usr/bin/bowtie2 --n-ceil 1.29192980533188,0.457777429330666 --score-min L,8.08425042040706,8.32144996212947 --gbar 1 --trim5 8 --np 3 -k 4 --trim3 1 --mp 5.04291744513809,2.91035187681201 --rdg 12.8964646156875 --local --cp-ival 1 --cp-min 3 -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw 1071s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 1071s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1071s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1071s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read '35' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1071s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read '49' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '61' because length (1) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1071s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 1071s Warning: skipping mate #2 of read '63' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '64' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '72' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '78' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '83' because length (1) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '86' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '88' because it was < 2 characters long 1071s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1071s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1071s Read 50 alignments... 1071s Read 100 alignments... 1071s 93 reads; of these: 1071s 78 (83.87%) were paired; of these: 1071s 78 (100.00%) aligned concordantly 0 times 1071s 0 (0.00%) aligned concordantly exactly 1 time 1071s 0 (0.00%) aligned concordantly >1 times 1071s ---- 1071s 78 pairs aligned concordantly 0 times; of these: 1071s 0 (0.00%) aligned discordantly 1 time 1071s ---- 1071s 78 pairs aligned 0 times concordantly or discordantly; of these: 1071s 156 mates make up the pairs; of these: 1071s 156 (100.00%) aligned 0 times 1071s 0 (0.00%) aligned exactly 1 time 1071s 0 (0.00%) aligned >1 times 1071s 15 (16.13%) were unpaired; of these: 1071s 15 (100.00%) aligned 0 times 1071s 0 (0.00%) aligned exactly 1 time 1071s 0 (0.00%) aligned >1 times 1071s 0.00% overall alignment rate 1071s Read 150 alignments... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s --- Summary --- 1071s Read 1 reference strings 1071s Checked 0 alignments, 0 edits 1071s --------------- 1071s PASSED 1071s Flattened IUPAC characters 1071s Mutating sequence Sim.pm.2 1071s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1071s Finished SNPs 1071s Finished ref gaps 1071s Finished read gaps 1071s Mutating sequence Sim.pm.1 1071s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1071s Finished SNPs 1071s Finished ref gaps 1071s Finished read gaps 1071s Mutated reference genome to subject genome 1071s SNPs introduced: 3 1071s Reference gaps introduced: 1 1071s Read gaps introduced: 1 1071s Rearrangements introduced: 0 1071s Created read sampler 1071s Sampling 147 reads 1071s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1071s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1071s parsing sequence Sim.pm.1... 1071s parsing sequence Sim.pm.2... 1071s Parsed 7 reference bases 1071s *** Run 28 of 100 1071s /usr/bin/bowtie2 --score-min L,5.95795280180219,8.25054722665647 --rfg 24.5823023000246 --trim5 4 --trim3 9 --mp 7.93992214738083,3.64618324298671 --mm -D 28 --cp-ival 1 --nofw --cp-min 2 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_139_139_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_141_141_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_145_145_1/1' because length (1) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 1071s 147 reads; of these: 1071s 147 (100.00%) were unpaired; of these: 1071s 141 (95.92%) aligned 0 times 1071s 6 (4.08%) aligned exactly 1 time 1071s 0 (0.00%) aligned >1 times 1071s 4.08% overall alignment rate 1071s Read 50 alignments... 1071s Read 100 alignments... 1071s Read 150 alignments... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s GT 1071s GT 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s AG 1071s AG 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s GT 1071s GT 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s GT 1071s GT 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s GGT 1071s GGT 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s GA 1071s GA 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s Processing line... 1071s --- Summary --- 1071s Read 1 reference strings 1071s Checked 6 alignments, 0 edits 1071s --------------- 1071s PASSED 1071s ALSO checking that bowtie2 and bowtie2-align match up 1071s /usr/bin/bowtie2 --score-min L,5.95795280180219,8.25054722665647 --rfg 24.5823023000246 --trim5 4 --trim3 9 --mp 7.93992214738083,3.64618324298671 --mm -D 28 --cp-ival 1 --nofw --cp-min 2 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_139_139_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_141_141_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 1071s 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 1071s Warning: skipping read 'R_1_1_1_145_145_1/1' because length (1) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 1071s 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 1071s 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 1071s Warning: skipping read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 1071s Warning: skipping read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 1071s 147 reads; of these: 1071s 147 (100.00%) were unpaired; of these: 1071s 141 (95.92%) aligned 0 times 1071s 6 (4.08%) aligned exactly 1 time 1071s 0 (0.00%) aligned >1 times 1071s 4.08% overall alignment rate 1071s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1071s Flattened IUPAC characters 1071s Mutating sequence Sim.pm.1 1071s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1071s Finished SNPs 1071s Finished ref gaps 1071s Finished read gaps 1071s Mutating sequence Sim.pm.2 1071s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1071s Finished SNPs 1071s Finished ref gaps 1071s Finished read gaps 1071s Mutated reference genome to subject genome 1071s SNPs introduced: 1 1071s Reference gaps introduced: 0 1071s Read gaps introduced: 0 1071s Rearrangements introduced: 0 1071s Created read sampler 1071s Sampling 72 reads 1072s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1072s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1072s parsing sequence Sim.pm.1... 1072s parsing sequence Sim.pm.2... 1072s Parsed 7 reference bases 1072s *** Run 29 of 100 1072s /usr/bin/bowtie2 --rfg 7.23568468542453 --local --rdg 15.8409462098407 -k 13 --score-min L,6.03435444315901,8.90393635669471 --cp-min 6 --mm -R 1 --cp-ival 1 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1072s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1072s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1072s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #2 of read '42' because it was < 2 characters long 1072s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1072s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '54' because it was < 2 characters long 1072s 72 reads; of these: 1072s 72 (100.00%) were paired; of these: 1072s 72 (100.00%) aligned concordantly 0 times 1072s 0 (0.00%) aligned concordantly exactly 1 time 1072s 0 (0.00%) aligned concordantly >1 times 1072s ---- 1072s 72 pairs aligned concordantly 0 times; of these: 1072s 0 (0.00%) aligned discordantly 1 time 1072s ---- 1072s 72 pairs aligned 0 times concordantly or discordantly; of these: 1072s 144 mates make up the pairs; of these: 1072s 144 (100.00%) aligned 0 times 1072s 0 (0.00%) aligned exactly 1 time 1072s 0 (0.00%) aligned >1 times 1072s 0.00% overall alignment rate 1072s Read 50 alignments... 1072s Read 100 alignments... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 1072s Processing line... 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1072s Processing line... 1072s Processing line... 1072s --- Summary --- 1072s Read 1 reference strings 1072s Checked 0 alignments, 0 edits 1072s --------------- 1072s PASSED 1072s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1072s /usr/bin/bowtie2 --rfg 7.23568468542453 --local --rdg 15.8409462098407 -k 13 --score-min L,6.03435444315901,8.90393635669471 --cp-min 6 --mm -R 1 --cp-ival 1 -f -p 2 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1072s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1072s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1072s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #2 of read '42' because it was < 2 characters long 1072s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1072s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '54' because it was < 2 characters long 1072s 72 reads; of these: 1072s 72 (100.00%) were paired; of these: 1072s 72 (100.00%) aligned concordantly 0 times 1072s 0 (0.00%) aligned concordantly exactly 1 time 1072s 0 (0.00%) aligned concordantly >1 times 1072s ---- 1072s 72 pairs aligned concordantly 0 times; of these: 1072s 0 (0.00%) aligned discordantly 1 time 1072s ---- 1072s 72 pairs aligned 0 times concordantly or discordantly; of these: 1072s 144 mates make up the pairs; of these: 1072s 144 (100.00%) aligned 0 times 1072s 0 (0.00%) aligned exactly 1 time 1072s 0 (0.00%) aligned >1 times 1072s 0.00% overall alignment rate 1072s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1072s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1072s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1072s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1072s /usr/bin/bowtie2 --rfg 7.23568468542453 --local --rdg 15.8409462098407 -k 13 --score-min L,6.03435444315901,8.90393635669471 --cp-min 6 --mm -R 1 --cp-ival 1 -f -p 4 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1072s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1072s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1072s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #2 of read '42' because it was < 2 characters long 1072s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1072s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 1072s Warning: skipping mate #1 of read '54' because it was < 2 characters long 1073s 72 reads; of these: 1073s 72 (100.00%) were paired; of these: 1073s 72 (100.00%) aligned concordantly 0 times 1073s 0 (0.00%) aligned concordantly exactly 1 time 1073s 0 (0.00%) aligned concordantly >1 times 1073s ---- 1073s 72 pairs aligned concordantly 0 times; of these: 1073s 0 (0.00%) aligned discordantly 1 time 1073s ---- 1073s 72 pairs aligned 0 times concordantly or discordantly; of these: 1073s 144 mates make up the pairs; of these: 1073s 144 (100.00%) aligned 0 times 1073s 0 (0.00%) aligned exactly 1 time 1073s 0 (0.00%) aligned >1 times 1073s 0.00% overall alignment rate 1073s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1073s Flattened IUPAC characters 1073s Mutating sequence Sim.pm.2 1073s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1073s Finished SNPs 1073s Finished ref gaps 1073s Finished read gaps 1073s Mutating sequence Sim.pm.1 1073s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1073s Finished SNPs 1073s Finished ref gaps 1073s Finished read gaps 1073s Mutated reference genome to subject genome 1073s SNPs introduced: 7 1073s Reference gaps introduced: 1 1073s Read gaps introduced: 0 1073s Rearrangements introduced: 0 1073s Created read sampler 1073s Sampling 28 reads 1073s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1073s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1073s parsing sequence Sim.pm.1... 1073s parsing sequence Sim.pm.2... 1073s *** Run 30 of 100 1073s /usr/bin/bowtie2 --cp-ival 1 --mm --np 7 --cp-min 2 --score-min L,5.28135098745806,8.92854865543853 --ma 20.079620159123 -M 2 --rdg 30.186488109106 -q -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq 1073s Parsed 7 reference bases 1073s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1073s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1073s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 1073s Warning: skipping read '3' because it was < 2 characters long 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1073s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 1073s Warning: skipping read '9' because it was < 2 characters long 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1073s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1073s Warning: skipping read '22' because it was < 2 characters long 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1073s 28 reads; of these: 1073s 28 (100.00%) were unpaired; of these: 1073s 27 (96.43%) aligned 0 times 1073s 1 (3.57%) aligned exactly 1 time 1073s 0 (0.00%) aligned >1 times 1073s 3.57% overall alignment rate 1073s Processing line... 1073s /usr/bin/bowtie2 --cp-ival 1 --mm --np 7 --cp-min 2 --score-min L,5.28135098745806,8.92854865543853 --ma 20.079620159123 -M 2 --rdg 30.186488109106 -q -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s GA 1073s GA 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s Processing line... 1073s --- Summary --- 1073s Read 1 reference strings 1073s Checked 1 alignments, 0 edits 1073s --------------- 1073s PASSED 1073s ALSO checking that bowtie2 and bowtie2-align match up 1073s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1073s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1073s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 1073s Warning: skipping read '3' because it was < 2 characters long 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1073s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 1073s Warning: skipping read '9' because it was < 2 characters long 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1073s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1073s Warning: skipping read '22' because it was < 2 characters long 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1073s 28 reads; of these: 1073s 28 (100.00%) were unpaired; of these: 1073s 27 (96.43%) aligned 0 times 1073s 1 (3.57%) aligned exactly 1 time 1073s 0 (0.00%) aligned >1 times 1073s 3.57% overall alignment rate 1073s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1073s /usr/bin/bowtie2 --cp-ival 1 --mm --np 7 --cp-min 2 --score-min L,5.28135098745806,8.92854865543853 --ma 20.079620159123 -M 2 --rdg 30.186488109106 -q -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1073s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1073s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1073s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1073s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 1073s Warning: skipping read '3' because it was < 2 characters long 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1073s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 1073s Warning: skipping read '9' because it was < 2 characters long 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1073s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1073s Warning: skipping read '22' because it was < 2 characters long 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1073s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1073s 28 reads; of these: 1073s 28 (100.00%) were unpaired; of these: 1073s 27 (96.43%) aligned 0 times 1073s 1 (3.57%) aligned exactly 1 time 1073s 0 (0.00%) aligned >1 times 1073s 3.57% overall alignment rate 1073s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1073s Flattened IUPAC characters 1073s Mutating sequence Sim.pm.2 1073s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1073s Finished SNPs 1073s Finished ref gaps 1073s Finished read gaps 1073s Mutating sequence Sim.pm.1 1073s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1073s Finished SNPs 1073s Finished ref gaps 1073s Finished read gaps 1073s Mutated reference genome to subject genome 1073s SNPs introduced: 5 1073s Reference gaps introduced: 1 1073s Read gaps introduced: 0 1073s Rearrangements introduced: 1 1073s Created read sampler 1073s Sampling 29 reads 1073s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1073s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1073s parsing sequence Sim.pm.1... 1073s parsing sequence Sim.pm.2... 1073s Parsed 7 reference bases 1073s *** Run 31 of 100 1073s /usr/bin/bowtie2 --local --rfg 32.3223676590255 --trim5 5 --rdg 17.620746206382,2.73206550219356 --score-min L,6.01855314270454,7.37361198419566 --norc --cp-min 4 --cp-ival 4 --mm -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1074s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '1' because it was < 2 characters long 1074s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1074s Warning: skipping read '2' because it was < 2 characters long 1074s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '3' because it was < 2 characters long 1074s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '7' because it was < 2 characters long 1074s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '8' because it was < 2 characters long 1074s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '10' because it was < 2 characters long 1074s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '15' because it was < 2 characters long 1074s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '17' because it was < 2 characters long 1074s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '25' because it was < 2 characters long 1074s 29 reads; of these: 1074s 29 (100.00%) were unpaired; of these: 1074s 29 (100.00%) aligned 0 times 1074s 0 (0.00%) aligned exactly 1 time 1074s 0 (0.00%) aligned >1 times 1074s 0.00% overall alignment rate 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s /usr/bin/bowtie2 --local --rfg 32.3223676590255 --trim5 5 --rdg 17.620746206382,2.73206550219356 --score-min L,6.01855314270454,7.37361198419566 --norc --cp-min 4 --cp-ival 4 --mm -f -p 4 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s --- Summary --- 1074s Read 1 reference strings 1074s Checked 0 alignments, 0 edits 1074s --------------- 1074s PASSED 1074s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1074s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '1' because it was < 2 characters long 1074s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1074s Warning: skipping read '2' because it was < 2 characters long 1074s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '3' because it was < 2 characters long 1074s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '7' because it was < 2 characters long 1074s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '8' because it was < 2 characters long 1074s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '10' because it was < 2 characters long 1074s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '15' because it was < 2 characters long 1074s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '17' because it was < 2 characters long 1074s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '25' because it was < 2 characters long 1074s 29 reads; of these: 1074s 29 (100.00%) were unpaired; of these: 1074s 29 (100.00%) aligned 0 times 1074s 0 (0.00%) aligned exactly 1 time 1074s 0 (0.00%) aligned >1 times 1074s 0.00% overall alignment rate 1074s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1074s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1074s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1074s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1074s /usr/bin/bowtie2 --local --rfg 32.3223676590255 --trim5 5 --rdg 17.620746206382,2.73206550219356 --score-min L,6.01855314270454,7.37361198419566 --norc --cp-min 4 --cp-ival 4 --mm -f -p 4 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1074s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '1' because it was < 2 characters long 1074s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1074s Warning: skipping read '2' because it was < 2 characters long 1074s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '3' because it was < 2 characters long 1074s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '7' because it was < 2 characters long 1074s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '8' because it was < 2 characters long 1074s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '10' because it was < 2 characters long 1074s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '15' because it was < 2 characters long 1074s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '17' because it was < 2 characters long 1074s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '25' because it was < 2 characters long 1074s 29 reads; of these: 1074s 29 (100.00%) were unpaired; of these: 1074s 29 (100.00%) aligned 0 times 1074s 0 (0.00%) aligned exactly 1 time 1074s 0 (0.00%) aligned >1 times 1074s 0.00% overall alignment rate 1074s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1074s Flattened IUPAC characters 1074s Mutating sequence Sim.pm.1 1074s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1074s Finished SNPs 1074s Finished ref gaps 1074s Finished read gaps 1074s Mutating sequence Sim.pm.2 1074s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1074s Finished SNPs 1074s Finished ref gaps 1074s Finished read gaps 1074s Mutated reference genome to subject genome 1074s SNPs introduced: 4 1074s Reference gaps introduced: 0 1074s Read gaps introduced: 0 1074s Rearrangements introduced: 0 1074s Created read sampler 1074s Sampling 99 reads 1074s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1074s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1074s parsing sequence Sim.pm.1... 1074s parsing sequence Sim.pm.2... 1074s Parsed 7 reference bases 1074s *** Run 32 of 100 1074s /usr/bin/bowtie2 --rfg 46.2057990801953,14.5273450602891 --trim3 8 --mp 9.36012211703248,6.90815855012903 --score-min L,6.41248893647527,3.38588212747126 --gbar 1 --np 2 --cp-min 12 --cp-ival 3 --mm -N 0 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1074s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '3' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1074s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '4' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1074s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1074s Warning: skipping read '10' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1074s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '14' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1074s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '16' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1074s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '18' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1074s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '21' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1074s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '22' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1074s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 1074s Warning: skipping read '28' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1074s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '29' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1074s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 1074s Warning: skipping read '31' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1074s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '33' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1074s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '34' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1074s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '35' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1074s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '36' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1074s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '39' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1074s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '40' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1074s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '42' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1074s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '43' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1074s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '44' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1074s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '47' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1074s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '48' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1074s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '50' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1074s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '53' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1074s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '56' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1074s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '59' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1074s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '60' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1074s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '61' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1074s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1074s Warning: skipping read '69' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1074s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '76' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1074s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '81' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1074s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '82' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1074s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '87' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1074s Warning: skipping read '91' because length (1) <= # seed mismatches (0) 1074s Warning: skipping read '91' because it was < 2 characters long 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1074s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1074s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1074s Warning: skipping read '98' because it was < 2 characters long 1074s 99 reads; of these: 1074s 99 (100.00%) were unpaired; of these: 1074s 95 (95.96%) aligned 0 times 1074s 4 (4.04%) aligned exactly 1 time 1074s 0 (0.00%) aligned >1 times 1074s 4.04% overall alignment rate 1074s Read 50 alignments... 1074s Read 100 alignments... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s GAG 1074s GAG 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s GG 1074s GG 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s AG 1074s AG 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s GA 1074s GA 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s Processing line... 1074s --- Summary --- 1074s Read 1 reference strings 1074s Checked 4 alignments, 0 edits 1074s --------------- 1074s PASSED 1074s Flattened IUPAC characters 1074s Mutating sequence Sim.pm.2 1074s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1074s Finished SNPs 1074s Finished ref gaps 1074s Finished read gaps 1074s Mutating sequence Sim.pm.1 1074s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1074s Finished SNPs 1074s Finished ref gaps 1074s Finished read gaps 1074s Mutated reference genome to subject genome 1074s SNPs introduced: 12 1074s Reference gaps introduced: 0 1074s Read gaps introduced: 0 1074s Rearrangements introduced: 1 1074s Created read sampler 1074s Sampling 50 reads 1075s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1075s *** Run 33 of 100 1075s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 2 --mp 2.05982724534595,1.72996270099973 --trim3 1 -R 2 --score-min L,7.27240672714756,6.61076194183657 --gbar 1 --rfg 34.7204701091349,12.9903027220516 --trim5 2 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1075s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1075s parsing sequence Sim.pm.1... 1075s parsing sequence Sim.pm.2... 1075s Parsed 7 reference bases 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1075s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 1075s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1075s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1075s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 1075s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 50 reads; of these: 1075s 48 (96.00%) were paired; of these: 1075s 48 (100.00%) aligned concordantly 0 times 1075s 0 (0.00%) aligned concordantly exactly 1 time 1075s 0 (0.00%) aligned concordantly >1 times 1075s ---- 1075s 48 pairs aligned concordantly 0 times; of these: 1075s 0 (0.00%) aligned discordantly 1 time 1075s ---- 1075s 48 pairs aligned 0 times concordantly or discordantly; of these: 1075s 96 mates make up the pairs; of these: 1075s 91 (94.79%) aligned 0 times 1075s 4 (4.17%) aligned exactly 1 time 1075s 1 (1.04%) aligned >1 times 1075s 2 (4.00%) were unpaired; of these: 1075s 1 (50.00%) aligned 0 times 1075s 1 (50.00%) aligned exactly 1 time 1075s 0 (0.00%) aligned >1 times 1075s 6.12% overall alignment rate 1075s Read 50 alignments... 1075s Read 100 alignments... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s TA 1075s TA 1075s Processing line... 1075s Processing line... 1075s GGTA 1075s GGTA 1075s Processing line... 1075s Processing line... 1075s GAGG 1075s GAGG 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s GA 1075s GA 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s GGT 1075s GGT 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s AG 1075s AG 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s --- Summary --- 1075s Read 1 reference strings 1075s Checked 6 alignments, 0 edits 1075s --------------- 1075s PASSED 1075s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1075s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 2 --mp 2.05982724534595,1.72996270099973 --trim3 1 -R 2 --score-min L,7.27240672714756,6.61076194183657 --gbar 1 --rfg 34.7204701091349,12.9903027220516 --trim5 2 --qseq -p 4 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1075s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 1075s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1075s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1075s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 1075s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 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 1075s 50 reads; of these: 1075s 48 (96.00%) were paired; of these: 1075s 48 (100.00%) aligned concordantly 0 times 1075s 0 (0.00%) aligned concordantly exactly 1 time 1075s 0 (0.00%) aligned concordantly >1 times 1075s ---- 1075s 48 pairs aligned concordantly 0 times; of these: 1075s 0 (0.00%) aligned discordantly 1 time 1075s ---- 1075s 48 pairs aligned 0 times concordantly or discordantly; of these: 1075s 96 mates make up the pairs; of these: 1075s 91 (94.79%) aligned 0 times 1075s 4 (4.17%) aligned exactly 1 time 1075s 1 (1.04%) aligned >1 times 1075s 2 (4.00%) were unpaired; of these: 1075s 1 (50.00%) aligned 0 times 1075s 1 (50.00%) aligned exactly 1 time 1075s 0 (0.00%) aligned >1 times 1075s 6.12% overall alignment rate 1075s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1075s Flattened IUPAC characters 1075s Mutating sequence Sim.pm.2 1075s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1075s Finished SNPs 1075s Finished ref gaps 1075s Finished read gaps 1075s Mutating sequence Sim.pm.1 1075s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1075s Finished SNPs 1075s Finished ref gaps 1075s Finished read gaps 1075s Mutated reference genome to subject genome 1075s SNPs introduced: 1 1075s Reference gaps introduced: 0 1075s Read gaps introduced: 0 1075s Rearrangements introduced: 0 1075s Created read sampler 1075s Sampling 111 reads 1075s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1075s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1075s parsing sequence Sim.pm.1... 1075s parsing sequence Sim.pm.2... 1075s Parsed 7 reference bases 1075s *** Run 34 of 100 1075s /usr/bin/bowtie2 -i S,0.674527798935242 --rfg 31.7005363113925 --trim5 8 --gbar 7 --score-min L,6.25061997133433,8.06897230160546 --n-ceil 1.26377496562007,0.0984081676531091 --cp-min 4 --cp-ival 1 --rdg 17.7310750857654,16.4998390043556 --mp 6.51110407218516,3.29836934262952 --trim3 7 -q -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1075s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '1' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1075s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '7' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1075s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '8' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1075s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '10' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1075s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '13' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1075s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '14' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1075s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '15' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1075s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '16' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1075s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '17' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1075s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '18' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1075s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '19' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1075s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '21' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1075s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '22' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1075s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '23' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1075s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '25' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1075s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 1075s Warning: skipping read '27' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1075s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '32' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1075s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '33' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1075s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 1075s Warning: skipping read '34' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1075s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 1075s Warning: skipping read '35' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1075s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '36' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1075s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '38' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1075s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '39' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1075s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 1075s Warning: skipping read '40' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1075s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '42' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1075s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '44' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1075s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '46' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1075s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '48' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1075s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '52' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1075s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '54' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1075s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '56' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1075s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '60' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1075s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '63' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1075s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '64' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1075s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '68' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1075s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '69' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1075s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '71' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1075s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '72' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1075s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '73' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1075s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '74' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1075s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '77' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1075s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '78' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1075s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '81' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1075s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '83' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1075s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '84' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1075s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '86' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1075s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '88' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1075s Warning: skipping read '90' because length (1) <= # seed mismatches (0) 1075s Warning: skipping read '90' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1075s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '91' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1075s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '92' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1075s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '94' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1075s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 1075s Warning: skipping read '96' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1075s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '97' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1075s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '98' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1075s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '101' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1075s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '102' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1075s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '105' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1075s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '107' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1075s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '109' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1075s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1075s Warning: skipping read '110' because it was < 2 characters long 1075s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1075s 111 reads; of these: 1075s 111 (100.00%) were unpaired; of these: 1075s 110 (99.10%) aligned 0 times 1075s 1 (0.90%) aligned exactly 1 time 1075s 0 (0.00%) aligned >1 times 1075s 0.90% overall alignment rate 1075s Read 50 alignments... 1075s Read 100 alignments... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s AG 1075s AG 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s Processing line... 1075s --- Summary --- 1075s Read 1 reference strings 1075s Checked 1 alignments, 0 edits 1075s --------------- 1075s PASSED 1075s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1075s /usr/bin/bowtie2 -i S,0.674527798935242 --rfg 31.7005363113925 --trim5 8 --gbar 7 --score-min L,6.25061997133433,8.06897230160546 --n-ceil 1.26377496562007,0.0984081676531091 --cp-min 4 --cp-ival 1 --rdg 17.7310750857654,16.4998390043556 --mp 6.51110407218516,3.29836934262952 --trim3 7 -q -p 4 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1076s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '1' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1076s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '7' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1076s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '8' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1076s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '10' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1076s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '13' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1076s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '14' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1076s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '15' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1076s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '16' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1076s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '33' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1076s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '34' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1076s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '35' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1076s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '36' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1076s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '38' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1076s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '39' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1076s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '40' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1076s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '42' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1076s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '44' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1076s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '46' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1076s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '48' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1076s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '52' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1076s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '54' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1076s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '56' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1076s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '60' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1076s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1076s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '17' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1076s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '18' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1076s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '19' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1076s Warning: skipping read '63' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1076s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '64' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1076s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '68' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1076s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '69' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1076s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '71' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1076s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '72' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1076s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '73' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1076s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '74' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1076s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '77' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1076s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '78' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1076s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '81' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1076s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '83' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1076s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '84' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1076s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '86' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1076s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '88' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1076s Warning: skipping read '90' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '90' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1076s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '91' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1076s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '92' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1076s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '94' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1076s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '96' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1076s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '97' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1076s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '98' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1076s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '101' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1076s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '102' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1076s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '105' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1076s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '107' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1076s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '109' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1076s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '110' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1076s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '21' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1076s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '22' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1076s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '23' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1076s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '25' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1076s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '27' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1076s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1076s Warning: skipping read '32' because it was < 2 characters long 1076s 111 reads; of these: 1076s 111 (100.00%) were unpaired; of these: 1076s 110 (99.10%) aligned 0 times 1076s 1 (0.90%) aligned exactly 1 time 1076s 0 (0.00%) aligned >1 times 1076s 0.90% overall alignment rate 1076s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1076s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1076s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1076s Flattened IUPAC characters 1076s Mutating sequence Sim.pm.2 1076s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1076s Finished SNPs 1076s Finished ref gaps 1076s Finished read gaps 1076s Mutating sequence Sim.pm.1 1076s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1076s Finished SNPs 1076s Finished ref gaps 1076s Finished read gaps 1076s Mutated reference genome to subject genome 1076s SNPs introduced: 1 1076s Reference gaps introduced: 0 1076s Read gaps introduced: 1 1076s Rearrangements introduced: 1 1076s Created read sampler 1076s Sampling 87 reads 1076s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1076s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1076s parsing sequence Sim.pm.1... 1076s parsing sequence Sim.pm.2... 1076s Parsed 7 reference bases 1076s *** Run 35 of 100 1076s /usr/bin/bowtie2 --cp-min 3 --cp-ival 2 --local --mp 9.24640278701868,4.6167468956781 --np 1 -N 1 -L18 --rfg 9.91467900748724,5.88292225033436 --trim5 8 --score-min L,4.62992112736371,2.29407840221965 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1076s Warning: skipping read '0' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '0' because it was < 2 characters long 1076s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '1' because it was < 2 characters long 1076s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '2' because it was < 2 characters long 1076s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '5' because it was < 2 characters long 1076s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '6' because it was < 2 characters long 1076s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '9' because it was < 2 characters long 1076s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '12' because it was < 2 characters long 1076s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '14' because it was < 2 characters long 1076s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '15' because it was < 2 characters long 1076s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '18' because it was < 2 characters long 1076s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '21' because it was < 2 characters long 1076s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '24' because it was < 2 characters long 1076s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '29' because it was < 2 characters long 1076s Warning: skipping read '34' because length (1) <= # seed mismatches (1) 1076s Warning: skipping read '34' because it was < 2 characters long 1076s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '37' because it was < 2 characters long 1076s Warning: skipping read '40' because length (1) <= # seed mismatches (1) 1076s Warning: skipping read '40' because it was < 2 characters long 1076s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '41' because it was < 2 characters long 1076s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '46' because it was < 2 characters long 1076s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '48' because it was < 2 characters long 1076s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '54' because it was < 2 characters long 1076s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '56' because it was < 2 characters long 1076s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '57' because it was < 2 characters long 1076s Warning: skipping read '60' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '60' because it was < 2 characters long 1076s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '61' because it was < 2 characters long 1076s Warning: skipping read '62' because length (1) <= # seed mismatches (1) 1076s Warning: skipping read '62' because it was < 2 characters long 1076s Warning: skipping read '64' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '64' because it was < 2 characters long 1076s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '65' because it was < 2 characters long 1076s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '70' because it was < 2 characters long 1076s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '75' because it was < 2 characters long 1076s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1076s Warning: skipping read '80' because it was < 2 characters long 1076s Warning: skipping read '81' because length (1) <= # seed mismatches (1) 1076s Warning: skipping read '81' because it was < 2 characters long 1076s 87 reads; of these: 1076s 87 (100.00%) were unpaired; of these: 1076s 87 (100.00%) aligned 0 times 1076s 0 (0.00%) aligned exactly 1 time 1076s 0 (0.00%) aligned >1 times 1076s 0.00% overall alignment rate 1076s Read 50 alignments... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s --- Summary --- 1076s Read 1 reference strings 1076s Checked 0 alignments, 0 edits 1076s --------------- 1076s PASSED 1076s Flattened IUPAC characters 1076s Mutating sequence Sim.pm.2 1076s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1076s Finished SNPs 1076s Finished ref gaps 1076s Finished read gaps 1076s Mutating sequence Sim.pm.1 1076s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1076s Finished SNPs 1076s Finished ref gaps 1076s Finished read gaps 1076s Mutated reference genome to subject genome 1076s SNPs introduced: 6 1076s Reference gaps introduced: 0 1076s Read gaps introduced: 0 1076s Rearrangements introduced: 0 1076s Created read sampler 1076s Sampling 94 reads 1076s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1076s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1076s parsing sequence Sim.pm.1... 1076s parsing sequence Sim.pm.2... 1076s Parsed 7 reference bases 1076s *** Run 36 of 100 1076s /usr/bin/bowtie2 -M 3 --rdg 6.25526669933352,7.91424104278464 --mm --cp-ival 2 --cp-min 8 --score-min L,1.8462334070028,5.66083738541751 -i L,0.0614982455630558 --rfg 37.1324685408081 -N 0 -L21 --norc -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1076s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1076s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '48' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1076s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '57' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1076s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '63' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1076s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '86' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1076s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '92' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1076s 94 reads; of these: 1076s 94 (100.00%) were unpaired; of these: 1076s 92 (97.87%) aligned 0 times 1076s 2 (2.13%) aligned exactly 1 time 1076s 0 (0.00%) aligned >1 times 1076s 2.13% overall alignment rate 1076s Read 50 alignments... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s AGG 1076s AGG 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s AG 1076s AG 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s Processing line... 1076s --- Summary --- 1076s Read 1 reference strings 1076s Checked 2 alignments, 0 edits 1076s --------------- 1076s PASSED 1076s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1076s /usr/bin/bowtie2 -M 3 --rdg 6.25526669933352,7.91424104278464 --mm --cp-ival 2 --cp-min 8 --score-min L,1.8462334070028,5.66083738541751 -i L,0.0614982455630558 --rfg 37.1324685408081 -N 0 -L21 --norc -r -p 4 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1076s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1076s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '48' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1076s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '86' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1076s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '92' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1076s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '57' because it was < 2 characters long 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1076s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1076s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 1076s Warning: skipping read '63' because it was < 2 characters long 1076s 94 reads; of these: 1076s 94 (100.00%) were unpaired; of these: 1076s 92 (97.87%) aligned 0 times 1076s 2 (2.13%) aligned exactly 1 time 1076s 0 (0.00%) aligned >1 times 1076s 2.13% overall alignment rate 1076s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1076s Flattened IUPAC characters 1076s Mutating sequence Sim.pm.2 1076s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1076s Finished SNPs 1076s Finished ref gaps 1076s Finished read gaps 1076s Mutating sequence Sim.pm.1 1076s Introducing 4 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1076s Finished SNPs 1076s Finished ref gaps 1076s Finished read gaps 1076s Mutated reference genome to subject genome 1076s SNPs introduced: 5 1076s Reference gaps introduced: 1 1076s Read gaps introduced: 1 1076s Rearrangements introduced: 0 1076s Created read sampler 1076s Sampling 85 reads 1076s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1076s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1076s parsing sequence Sim.pm.1... 1076s parsing sequence Sim.pm.2... 1076s Parsed 7 reference bases 1076s *** Run 37 of 100 1076s /usr/bin/bowtie2 -M 4 --score-min L,6.50877339590608,9.43848786050057 --mp 6.85593523027119,5.28926716306606 --rdg 20.6068258446549 --trim5 2 --cp-ival 1 -D 43 --cp-min 2 --nofw --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1077s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1077s 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 1077s 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 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s 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 1077s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (0) 1077s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 1077s 85 reads; of these: 1077s 85 (100.00%) were unpaired; of these: 1077s 85 (100.00%) aligned 0 times 1077s 0 (0.00%) aligned exactly 1 time 1077s 0 (0.00%) aligned >1 times 1077s 0.00% overall alignment rate 1077s Read 50 alignments... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s --- Summary --- 1077s Read 1 reference strings 1077s Checked 0 alignments, 0 edits 1077s --------------- 1077s PASSED 1077s Flattened IUPAC characters 1077s Mutating sequence Sim.pm.2 1077s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1077s Finished SNPs 1077s Finished ref gaps 1077s Finished read gaps 1077s Mutating sequence Sim.pm.1 1077s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1077s Finished SNPs 1077s Finished ref gaps 1077s Finished read gaps 1077s Mutated reference genome to subject genome 1077s SNPs introduced: 1 1077s Reference gaps introduced: 0 1077s Read gaps introduced: 0 1077s Rearrangements introduced: 1 1077s Created read sampler 1077s Sampling 92 reads 1077s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1077s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1077s parsing sequence Sim.pm.1... 1077s *** Run 38 of 100 1077s /usr/bin/bowtie2 -R 1 -N 0 -L19 --score-min L,4.97220766946564,2.45517035652394 --n-ceil 0.201574621784428,0.184672607666427 -i S,2.41194983060273 --trim5 2 --cp-ival 1 --cp-min 15 -k 2 --local --trim3 2 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1077s parsing sequence Sim.pm.2... 1077s Parsed 7 reference bases 1077s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '11' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1077s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 1077s Warning: skipping mate #2 of read '21' because it was < 2 characters long 1077s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 1077s Warning: skipping mate #2 of read '22' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1077s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (0) 1077s Warning: skipping mate #2 of read '47' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1077s Read 50 alignments... 1077s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '82' because it was < 2 characters long 1077s Read 100 alignments... 1077s 92 reads; of these: 1077s 81 (88.04%) were paired; of these: 1077s 81 (100.00%) aligned concordantly 0 times 1077s 0 (0.00%) aligned concordantly exactly 1 time 1077s 0 (0.00%) aligned concordantly >1 times 1077s ---- 1077s 81 pairs aligned concordantly 0 times; of these: 1077s 0 (0.00%) aligned discordantly 1 time 1077s ---- 1077s 81 pairs aligned 0 times concordantly or discordantly; of these: 1077s 162 mates make up the pairs; of these: 1077s 162 (100.00%) aligned 0 times 1077s 0 (0.00%) aligned exactly 1 time 1077s 0 (0.00%) aligned >1 times 1077s 11 (11.96%) were unpaired; of these: 1077s 11 (100.00%) aligned 0 times 1077s 0 (0.00%) aligned exactly 1 time 1077s 0 (0.00%) aligned >1 times 1077s 0.00% overall alignment rate 1077s Read 150 alignments... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s /usr/bin/bowtie2 -R 1 -N 0 -L19 --score-min L,4.97220766946564,2.45517035652394 --n-ceil 0.201574621784428,0.184672607666427 -i S,2.41194983060273 --trim5 2 --cp-ival 1 --cp-min 15 -k 2 --local --trim3 2 -q -p 4 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s Processing line... 1077s --- Summary --- 1077s Read 1 reference strings 1077s Checked 0 alignments, 0 edits 1077s --------------- 1077s PASSED 1077s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1077s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '11' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1077s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (0) 1077s Warning: skipping mate #2 of read '47' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1077s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 1077s Warning: skipping mate #2 of read '21' because it was < 2 characters long 1077s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 1077s Warning: skipping mate #2 of read '22' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '82' because it was < 2 characters long 1077s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1077s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1077s 92 reads; of these: 1077s 81 (88.04%) were paired; of these: 1077s 81 (100.00%) aligned concordantly 0 times 1077s 0 (0.00%) aligned concordantly exactly 1 time 1077s 0 (0.00%) aligned concordantly >1 times 1077s ---- 1077s 81 pairs aligned concordantly 0 times; of these: 1077s 0 (0.00%) aligned discordantly 1 time 1077s ---- 1077s 81 pairs aligned 0 times concordantly or discordantly; of these: 1077s 162 mates make up the pairs; of these: 1077s 162 (100.00%) aligned 0 times 1077s 0 (0.00%) aligned exactly 1 time 1077s 0 (0.00%) aligned >1 times 1077s 11 (11.96%) were unpaired; of these: 1077s 11 (100.00%) aligned 0 times 1077s 0 (0.00%) aligned exactly 1 time 1077s 0 (0.00%) aligned >1 times 1077s 0.00% overall alignment rate 1078s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1078s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1078s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1078s Flattened IUPAC characters 1078s Mutating sequence Sim.pm.2 1078s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1078s Finished SNPs 1078s Finished ref gaps 1078s Finished read gaps 1078s Mutating sequence Sim.pm.1 1078s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1078s Finished SNPs 1078s Finished ref gaps 1078s Finished read gaps 1078s Mutated reference genome to subject genome 1078s SNPs introduced: 9 1078s Reference gaps introduced: 0 1078s Read gaps introduced: 0 1078s Rearrangements introduced: 0 1078s Created read sampler 1078s Sampling 80 reads 1078s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1078s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1078s parsing sequence Sim.pm.1... 1078s parsing sequence Sim.pm.2... 1078s Parsed 7 reference bases 1078s *** Run 39 of 100 1078s /usr/bin/bowtie2 --cp-min 5 --cp-ival 4 --mm --local -k 3 --np 1 --norc -D 34 --trim5 9 --score-min L,7.12036313825793,6.31168575095632 -q -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq 1078s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '1' because it was < 2 characters long 1078s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '3' because it was < 2 characters long 1078s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '5' because it was < 2 characters long 1078s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '7' because it was < 2 characters long 1078s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '9' because it was < 2 characters long 1078s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '14' because it was < 2 characters long 1078s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '18' because it was < 2 characters long 1078s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '21' because it was < 2 characters long 1078s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '22' because it was < 2 characters long 1078s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '28' because it was < 2 characters long 1078s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '29' because it was < 2 characters long 1078s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '30' because it was < 2 characters long 1078s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '31' because it was < 2 characters long 1078s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '35' because it was < 2 characters long 1078s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '37' because it was < 2 characters long 1078s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '40' because it was < 2 characters long 1078s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '42' because it was < 2 characters long 1078s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '43' because it was < 2 characters long 1078s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '46' because it was < 2 characters long 1078s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '47' because it was < 2 characters long 1078s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1078s Warning: skipping read '56' because it was < 2 characters long 1078s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '63' because it was < 2 characters long 1078s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '68' because it was < 2 characters long 1078s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1078s Warning: skipping read '69' because it was < 2 characters long 1078s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '72' because it was < 2 characters long 1078s 80 reads; of these: 1078s 80 (100.00%) were unpaired; of these: 1078s 80 (100.00%) aligned 0 times 1078s 0 (0.00%) aligned exactly 1 time 1078s 0 (0.00%) aligned >1 times 1078s 0.00% overall alignment rate 1078s Read 50 alignments... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s Processing line... 1078s --- Summary --- 1078s Read 1 reference strings 1078s Checked 0 alignments, 0 edits 1078s --------------- 1078s PASSED 1078s ALSO checking that bowtie2 and bowtie2-align match up 1078s /usr/bin/bowtie2 --cp-min 5 --cp-ival 4 --mm --local -k 3 --np 1 --norc -D 34 --trim5 9 --score-min L,7.12036313825793,6.31168575095632 -q -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1078s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '1' because it was < 2 characters long 1078s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '3' because it was < 2 characters long 1078s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '5' because it was < 2 characters long 1078s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '7' because it was < 2 characters long 1078s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '9' because it was < 2 characters long 1078s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '14' because it was < 2 characters long 1078s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '18' because it was < 2 characters long 1078s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '21' because it was < 2 characters long 1078s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '22' because it was < 2 characters long 1078s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '28' because it was < 2 characters long 1078s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '29' because it was < 2 characters long 1078s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '30' because it was < 2 characters long 1078s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '31' because it was < 2 characters long 1078s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '35' because it was < 2 characters long 1078s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '37' because it was < 2 characters long 1078s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '40' because it was < 2 characters long 1078s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '42' because it was < 2 characters long 1078s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '43' because it was < 2 characters long 1078s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '46' because it was < 2 characters long 1078s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '47' because it was < 2 characters long 1078s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1078s Warning: skipping read '56' because it was < 2 characters long 1078s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '63' because it was < 2 characters long 1078s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '68' because it was < 2 characters long 1078s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1078s Warning: skipping read '69' because it was < 2 characters long 1078s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '72' because it was < 2 characters long 1078s 80 reads; of these: 1078s 80 (100.00%) were unpaired; of these: 1078s 80 (100.00%) aligned 0 times 1078s 0 (0.00%) aligned exactly 1 time 1078s 0 (0.00%) aligned >1 times 1078s 0.00% overall alignment rate 1078s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1078s /usr/bin/bowtie2 --cp-min 5 --cp-ival 4 --mm --local -k 3 --np 1 --norc -D 34 --trim5 9 --score-min L,7.12036313825793,6.31168575095632 -q -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1078s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1078s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '1' because it was < 2 characters long 1078s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '3' because it was < 2 characters long 1078s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '5' because it was < 2 characters long 1078s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '7' because it was < 2 characters long 1078s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '9' because it was < 2 characters long 1078s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '14' because it was < 2 characters long 1078s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '18' because it was < 2 characters long 1078s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '21' because it was < 2 characters long 1078s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '22' because it was < 2 characters long 1078s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '28' because it was < 2 characters long 1078s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '29' because it was < 2 characters long 1078s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '30' because it was < 2 characters long 1078s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '31' because it was < 2 characters long 1078s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '35' because it was < 2 characters long 1078s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '37' because it was < 2 characters long 1078s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '40' because it was < 2 characters long 1078s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '42' because it was < 2 characters long 1078s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '43' because it was < 2 characters long 1078s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '46' because it was < 2 characters long 1078s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '47' because it was < 2 characters long 1078s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '68' because it was < 2 characters long 1078s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 1078s Warning: skipping read '69' because it was < 2 characters long 1078s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '72' because it was < 2 characters long 1078s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1078s Warning: skipping read '56' because it was < 2 characters long 1078s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1078s Warning: skipping read '63' because it was < 2 characters long 1078s 80 reads; of these: 1078s 80 (100.00%) were unpaired; of these: 1078s 80 (100.00%) aligned 0 times 1078s 0 (0.00%) aligned exactly 1 time 1078s 0 (0.00%) aligned >1 times 1078s 0.00% overall alignment rate 1078s Flattened IUPAC characters 1078s Mutating sequence Sim.pm.2 1078s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1078s Finished SNPs 1078s Finished ref gaps 1078s Finished read gaps 1078s Mutating sequence Sim.pm.1 1078s Introducing 13 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1078s Finished SNPs 1078s Finished ref gaps 1078s Finished read gaps 1078s Mutated reference genome to subject genome 1078s SNPs introduced: 17 1078s Reference gaps introduced: 0 1078s Read gaps introduced: 0 1078s Rearrangements introduced: 0 1078s Created read sampler 1078s Sampling 72 reads 1078s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1078s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1078s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1078s parsing sequence Sim.pm.1... 1078s parsing sequence Sim.pm.2... 1078s Parsed 7 reference bases 1078s *** Run 40 of 100 1078s /usr/bin/bowtie2 -D 40 --np 9 --n-ceil 0.901856571509414,1.38467024438873 --gbar 1 --score-min L,5.72633876359965,5.69227496341028 --trim5 9 --mm --cp-ival 1 --cp-min 8 --ma 1.23892828696822 -k 2 --mp 8.14374926603338,6.07480466708466 -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw 1079s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1079s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1079s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1079s Warning: skipping read '4' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1079s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1079s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1079s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1079s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1079s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1079s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1079s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1079s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1079s 72 reads; of these: 1079s 60 (83.33%) were paired; of these: 1079s 60 (100.00%) aligned concordantly 0 times 1079s 0 (0.00%) aligned concordantly exactly 1 time 1079s 0 (0.00%) aligned concordantly >1 times 1079s ---- 1079s 60 pairs aligned concordantly 0 times; of these: 1079s 0 (0.00%) aligned discordantly 1 time 1079s ---- 1079s 60 pairs aligned 0 times concordantly or discordantly; of these: 1079s 120 mates make up the pairs; of these: 1079s 117 (97.50%) aligned 0 times 1079s 3 (2.50%) aligned exactly 1 time 1079s 0 (0.00%) aligned >1 times 1079s 12 (16.67%) were unpaired; of these: 1079s 11 (91.67%) aligned 0 times 1079s 1 (8.33%) aligned exactly 1 time 1079s 0 (0.00%) aligned >1 times 1079s 3.03% overall alignment rate 1079s Read 50 alignments... 1079s Read 100 alignments... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s GA 1079s GA 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s AGG 1079s AGG 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s GT 1079s GT 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s GT 1079s GT 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s /usr/bin/bowtie2 -D 40 --np 9 --n-ceil 0.901856571509414,1.38467024438873 --gbar 1 --score-min L,5.72633876359965,5.69227496341028 --trim5 9 --mm --cp-ival 1 --cp-min 8 --ma 1.23892828696822 -k 2 --mp 8.14374926603338,6.07480466708466 -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s Processing line... 1079s --- Summary --- 1079s Read 1 reference strings 1079s Checked 4 alignments, 0 edits 1079s --------------- 1079s PASSED 1079s ALSO checking that bowtie2 and bowtie2-align match up 1079s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1079s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1079s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1079s Warning: skipping read '4' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1079s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1079s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1079s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1079s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1079s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1079s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1079s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1079s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1079s 72 reads; of these: 1079s 60 (83.33%) were paired; of these: 1079s 60 (100.00%) aligned concordantly 0 times 1079s 0 (0.00%) aligned concordantly exactly 1 time 1079s 0 (0.00%) aligned concordantly >1 times 1079s ---- 1079s 60 pairs aligned concordantly 0 times; of these: 1079s 0 (0.00%) aligned discordantly 1 time 1079s ---- 1079s 60 pairs aligned 0 times concordantly or discordantly; of these: 1079s 120 mates make up the pairs; of these: 1079s 117 (97.50%) aligned 0 times 1079s 3 (2.50%) aligned exactly 1 time 1079s 0 (0.00%) aligned >1 times 1079s 12 (16.67%) were unpaired; of these: 1079s 11 (91.67%) aligned 0 times 1079s 1 (8.33%) aligned exactly 1 time 1079s 0 (0.00%) aligned >1 times 1079s 3.03% overall alignment rate 1079s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1079s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1079s /usr/bin/bowtie2 -D 40 --np 9 --n-ceil 0.901856571509414,1.38467024438873 --gbar 1 --score-min L,5.72633876359965,5.69227496341028 --trim5 9 --mm --cp-ival 1 --cp-min 8 --ma 1.23892828696822 -k 2 --mp 8.14374926603338,6.07480466708466 -r -p 4 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1079s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1079s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1079s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1079s Warning: skipping read '4' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1079s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1079s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1079s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1079s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1079s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1079s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1079s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1079s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1079s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1079s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1079s 72 reads; of these: 1079s 60 (83.33%) were paired; of these: 1079s 60 (100.00%) aligned concordantly 0 times 1079s 0 (0.00%) aligned concordantly exactly 1 time 1079s 0 (0.00%) aligned concordantly >1 times 1079s ---- 1079s 60 pairs aligned concordantly 0 times; of these: 1079s 0 (0.00%) aligned discordantly 1 time 1079s ---- 1079s 60 pairs aligned 0 times concordantly or discordantly; of these: 1079s 120 mates make up the pairs; of these: 1079s 117 (97.50%) aligned 0 times 1079s 3 (2.50%) aligned exactly 1 time 1079s 0 (0.00%) aligned >1 times 1079s 12 (16.67%) were unpaired; of these: 1079s 11 (91.67%) aligned 0 times 1079s 1 (8.33%) aligned exactly 1 time 1079s 0 (0.00%) aligned >1 times 1079s 3.03% overall alignment rate 1079s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1079s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1079s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1079s Flattened IUPAC characters 1079s Mutating sequence Sim.pm.2 1079s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1079s Finished SNPs 1079s Finished ref gaps 1079s Finished read gaps 1079s Mutating sequence Sim.pm.1 1079s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1079s Finished SNPs 1079s Finished ref gaps 1079s Finished read gaps 1079s Mutated reference genome to subject genome 1079s SNPs introduced: 8 1079s Reference gaps introduced: 1 1079s Read gaps introduced: 0 1079s Rearrangements introduced: 0 1079s Created read sampler 1079s Sampling 116 reads 1079s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1079s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1079s parsing sequence Sim.pm.1... 1079s parsing sequence Sim.pm.2... 1079s Parsed 7 reference bases 1079s *** Run 41 of 100 1079s /usr/bin/bowtie2 --mp 2.39294003713872,1.24072856198155 -a --cp-min 5 --cp-ival 5 --mm -i C,3.95560651841879 --score-min L,2.88793347844591,6.25263069359288 --nofw --np 1 --norc -N 0 -L20 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Read 50 alignments... 1080s Read 100 alignments... 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_99_99_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_102_102_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 116 reads; of these: 1080s 116 (100.00%) were paired; of these: 1080s 116 (100.00%) aligned concordantly 0 times 1080s 0 (0.00%) aligned concordantly exactly 1 time 1080s 0 (0.00%) aligned concordantly >1 times 1080s ---- 1080s 116 pairs aligned concordantly 0 times; of these: 1080s 0 (0.00%) aligned discordantly 1 time 1080s ---- 1080s 116 pairs aligned 0 times concordantly or discordantly; of these: 1080s 232 mates make up the pairs; of these: 1080s 232 (100.00%) aligned 0 times 1080s 0 (0.00%) aligned exactly 1 time 1080s 0 (0.00%) aligned >1 times 1080s 0.00% overall alignment rate 1080s Read 150 alignments... 1080s Read 200 alignments... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s /usr/bin/bowtie2 --mp 2.39294003713872,1.24072856198155 -a --cp-min 5 --cp-ival 5 --mm -i C,3.95560651841879 --score-min L,2.88793347844591,6.25263069359288 --nofw --np 1 --norc -N 0 -L20 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s --- Summary --- 1080s Read 1 reference strings 1080s Checked 0 alignments, 0 edits 1080s --------------- 1080s PASSED 1080s ALSO checking that bowtie2 and bowtie2-align match up 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_99_99_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_102_102_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 116 reads; of these: 1080s 116 (100.00%) were paired; of these: 1080s 116 (100.00%) aligned concordantly 0 times 1080s 0 (0.00%) aligned concordantly exactly 1 time 1080s 0 (0.00%) aligned concordantly >1 times 1080s ---- 1080s 116 pairs aligned concordantly 0 times; of these: 1080s 0 (0.00%) aligned discordantly 1 time 1080s ---- 1080s 116 pairs aligned 0 times concordantly or discordantly; of these: 1080s 232 mates make up the pairs; of these: 1080s 232 (100.00%) aligned 0 times 1080s 0 (0.00%) aligned exactly 1 time 1080s 0 (0.00%) aligned >1 times 1080s 0.00% overall alignment rate 1080s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1080s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1080s /usr/bin/bowtie2 --mp 2.39294003713872,1.24072856198155 -a --cp-min 5 --cp-ival 5 --mm -i C,3.95560651841879 --score-min L,2.88793347844591,6.25263069359288 --nofw --np 1 --norc -N 0 -L20 --qseq -p 2 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_99_99_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_102_102_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 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 1080s 116 reads; of these: 1080s 116 (100.00%) were paired; of these: 1080s 116 (100.00%) aligned concordantly 0 times 1080s 0 (0.00%) aligned concordantly exactly 1 time 1080s 0 (0.00%) aligned concordantly >1 times 1080s ---- 1080s 116 pairs aligned concordantly 0 times; of these: 1080s 0 (0.00%) aligned discordantly 1 time 1080s ---- 1080s 116 pairs aligned 0 times concordantly or discordantly; of these: 1080s 232 mates make up the pairs; of these: 1080s 232 (100.00%) aligned 0 times 1080s 0 (0.00%) aligned exactly 1 time 1080s 0 (0.00%) aligned >1 times 1080s 0.00% overall alignment rate 1080s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1080s Flattened IUPAC characters 1080s Mutating sequence Sim.pm.1 1080s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1080s Finished SNPs 1080s Finished ref gaps 1080s Finished read gaps 1080s Mutating sequence Sim.pm.2 1080s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1080s Finished SNPs 1080s Finished ref gaps 1080s Finished read gaps 1080s Mutated reference genome to subject genome 1080s SNPs introduced: 4 1080s Reference gaps introduced: 0 1080s Read gaps introduced: 0 1080s Rearrangements introduced: 0 1080s Created read sampler 1080s Sampling 51 reads 1080s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1080s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1080s parsing sequence Sim.pm.1... 1080s parsing sequence Sim.pm.2... 1080s Parsed 7 reference bases 1080s *** Run 42 of 100 1080s /usr/bin/bowtie2 --np 1 --rfg 4.71147315878198 --trim5 8 --score-min L,2.94626642644063,3.84635790946913 --cp-min 3 --cp-ival 1 --mm --trim3 3 --mp 8.57152978637257,2.84337154947528 --ma 19.2911341892306 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1080s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1080s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read '1' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1080s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1080s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1080s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1080s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1080s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 1080s Warning: skipping mate #2 of read '13' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1080s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1080s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '25' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1080s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1080s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1080s Warning: skipping read '30' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1080s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1080s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1080s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1080s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1080s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 1080s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1080s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 1080s Warning: skipping read '48' because it was < 2 characters long 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1080s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1080s 51 reads; of these: 1080s 43 (84.31%) were paired; of these: 1080s 43 (100.00%) aligned concordantly 0 times 1080s 0 (0.00%) aligned concordantly exactly 1 time 1080s 0 (0.00%) aligned concordantly >1 times 1080s ---- 1080s 43 pairs aligned concordantly 0 times; of these: 1080s 1 (2.33%) aligned discordantly 1 time 1080s ---- 1080s 42 pairs aligned 0 times concordantly or discordantly; of these: 1080s 84 mates make up the pairs; of these: 1080s 82 (97.62%) aligned 0 times 1080s 2 (2.38%) aligned exactly 1 time 1080s 0 (0.00%) aligned >1 times 1080s 8 (15.69%) were unpaired; of these: 1080s 8 (100.00%) aligned 0 times 1080s 0 (0.00%) aligned exactly 1 time 1080s 0 (0.00%) aligned >1 times 1080s 4.26% overall alignment rate 1080s Read 50 alignments... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s GGT 1080s GGT 1080s Processing line... 1080s AG 1080s AG 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s GG 1080s GG 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s GT 1080s GT 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s Processing line... 1080s --- Summary --- 1080s Read 1 reference strings 1080s Checked 4 alignments, 0 edits 1080s --------------- 1080s PASSED 1080s Flattened IUPAC characters 1080s Mutating sequence Sim.pm.1 1080s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1080s Finished SNPs 1080s Finished ref gaps 1080s Finished read gaps 1080s Mutating sequence Sim.pm.2 1080s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1080s Finished SNPs 1080s Finished ref gaps 1080s Finished read gaps 1080s Mutated reference genome to subject genome 1080s SNPs introduced: 4 1080s Reference gaps introduced: 0 1080s Read gaps introduced: 0 1080s Rearrangements introduced: 1 1080s Created read sampler 1080s Sampling 120 reads 1081s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1081s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1081s parsing sequence Sim.pm.1... 1081s parsing sequence Sim.pm.2... 1081s Parsed 7 reference bases 1081s *** Run 43 of 100 1081s /usr/bin/bowtie2 --trim3 3 --mp 6.87940266577025,4.75381654504426 --score-min L,3.93438805054081,6.26453242659814 --n-ceil 1.02466994342252,0.835123793913761 --np 2 --cp-min 3 --cp-ival 2 --mm -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1081s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 1081s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1081s Warning: skipping mate #1 of read '4' because length (1) <= # seed mismatches (0) 1081s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1081s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 1081s Warning: skipping mate #2 of read '9' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1081s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1081s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1081s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 1081s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1081s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '56' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1081s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (0) 1081s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1081s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 1081s Warning: skipping mate #1 of read '77' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1081s Warning: skipping mate #2 of read '79' because length (1) <= # seed mismatches (0) 1081s Warning: skipping mate #2 of read '79' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1081s Read 50 alignments... 1081s Read 100 alignments... 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1081s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 1081s Warning: skipping mate #1 of read '92' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1081s Warning: skipping mate #1 of read '93' because length (1) <= # seed mismatches (0) 1081s Warning: skipping mate #1 of read '93' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1081s Warning: skipping mate #1 of read '118' because length (1) <= # seed mismatches (0) 1081s Warning: skipping mate #1 of read '118' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1081s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 1081s Warning: skipping mate #1 of read '119' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1081s 120 reads; of these: 1081s 113 (94.17%) were paired; of these: 1081s 113 (100.00%) aligned concordantly 0 times 1081s 0 (0.00%) aligned concordantly exactly 1 time 1081s 0 (0.00%) aligned concordantly >1 times 1081s ---- 1081s 113 pairs aligned concordantly 0 times; of these: 1081s 0 (0.00%) aligned discordantly 1 time 1081s ---- 1081s 113 pairs aligned 0 times concordantly or discordantly; of these: 1081s 226 mates make up the pairs; of these: 1081s 220 (97.35%) aligned 0 times 1081s 6 (2.65%) aligned exactly 1 time 1081s 0 (0.00%) aligned >1 times 1081s 7 (5.83%) were unpaired; of these: 1081s 7 (100.00%) aligned 0 times 1081s 0 (0.00%) aligned exactly 1 time 1081s 0 (0.00%) aligned >1 times 1081s 2.58% overall alignment rate 1081s Read 150 alignments... 1081s Read 200 alignments... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s GA 1081s GA 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s GAGGTA 1081s GAGGTA 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s GT 1081s GT 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s GT 1081s GT 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s GG 1081s GG 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s GG 1081s GG 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s --- Summary --- 1081s Read 1 reference strings 1081s Checked 6 alignments, 0 edits 1081s --------------- 1081s PASSED 1081s Flattened IUPAC characters 1081s Mutating sequence Sim.pm.1 1081s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1081s Finished SNPs 1081s Finished ref gaps 1081s Finished read gaps 1081s Mutating sequence Sim.pm.2 1081s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1081s Finished SNPs 1081s Finished ref gaps 1081s Finished read gaps 1081s Mutated reference genome to subject genome 1081s SNPs introduced: 3 1081s Reference gaps introduced: 1 1081s Read gaps introduced: 0 1081s Rearrangements introduced: 1 1081s Created read sampler 1081s Sampling 71 reads 1081s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1081s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1081s *** Run 44 of 100 1081s /usr/bin/bowtie2 --gbar 6 -k 2 --score-min L,4.88396357192514,4.41604811296058 --mp 6.11521101593642,5.92702853996187 --mm --cp-ival 1 --cp-min 4 --np 3 --nofw -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1081s parsing sequence Sim.pm.1... 1081s parsing sequence Sim.pm.2... 1081s Parsed 7 reference bases 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1081s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 1081s Warning: skipping mate #2 of read '28' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1081s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 1081s Warning: skipping mate #2 of read '37' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1081s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 1081s Warning: skipping mate #2 of read '54' because it was < 2 characters long 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1081s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1081s 71 reads; of these: 1081s 71 (100.00%) were paired; of these: 1081s 71 (100.00%) aligned concordantly 0 times 1081s 0 (0.00%) aligned concordantly exactly 1 time 1081s 0 (0.00%) aligned concordantly >1 times 1081s ---- 1081s 71 pairs aligned concordantly 0 times; of these: 1081s 0 (0.00%) aligned discordantly 1 time 1081s ---- 1081s 71 pairs aligned 0 times concordantly or discordantly; of these: 1081s 142 mates make up the pairs; of these: 1081s 140 (98.59%) aligned 0 times 1081s 2 (1.41%) aligned exactly 1 time 1081s 0 (0.00%) aligned >1 times 1081s 1.41% overall alignment rate 1081s Read 50 alignments... 1081s Read 100 alignments... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s AGGTA 1081s AGGTA 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s GG 1081s GG 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s --- Summary --- 1081s Read 1 reference strings 1081s Checked 2 alignments, 0 edits 1081s --------------- 1081s PASSED 1081s Flattened IUPAC characters 1081s Mutating sequence Sim.pm.2 1081s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1081s Finished SNPs 1081s Finished ref gaps 1081s Finished read gaps 1081s Mutating sequence Sim.pm.1 1081s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1081s Finished SNPs 1081s Finished ref gaps 1081s Finished read gaps 1081s Mutated reference genome to subject genome 1081s SNPs introduced: 1 1081s Reference gaps introduced: 0 1081s Read gaps introduced: 0 1081s Rearrangements introduced: 0 1081s Created read sampler 1081s Sampling 157 reads 1081s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1081s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1081s parsing sequence Sim.pm.1... 1081s parsing sequence Sim.pm.2... 1081s Parsed 7 reference bases 1081s *** Run 45 of 100 1081s /usr/bin/bowtie2 --score-min L,4.47888362673349,1.39191741464333 --n-ceil 1.02585625657708,0.266162230690843 --local --trim3 7 -a --trim5 7 --cp-ival 1 --mm --nofw --np 5 --cp-min 7 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1081s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '2' because it was < 2 characters long 1081s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '3' because it was < 2 characters long 1081s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '5' because it was < 2 characters long 1081s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '8' because it was < 2 characters long 1081s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '10' because it was < 2 characters long 1081s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '11' because it was < 2 characters long 1081s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '14' because it was < 2 characters long 1081s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '15' because it was < 2 characters long 1081s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '19' because it was < 2 characters long 1081s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '20' because it was < 2 characters long 1081s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '22' because it was < 2 characters long 1081s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '23' because it was < 2 characters long 1081s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '26' because it was < 2 characters long 1081s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '30' because it was < 2 characters long 1081s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '33' because it was < 2 characters long 1081s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '34' because it was < 2 characters long 1081s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '35' because it was < 2 characters long 1081s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '36' because it was < 2 characters long 1081s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 1081s Warning: skipping read '37' because it was < 2 characters long 1081s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '38' because it was < 2 characters long 1081s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '39' because it was < 2 characters long 1081s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '40' because it was < 2 characters long 1081s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '56' because it was < 2 characters long 1081s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '57' because it was < 2 characters long 1081s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '60' because it was < 2 characters long 1081s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '61' because it was < 2 characters long 1081s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '66' because it was < 2 characters long 1081s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '67' because it was < 2 characters long 1081s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '68' because it was < 2 characters long 1081s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '69' because it was < 2 characters long 1081s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '72' because it was < 2 characters long 1081s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '73' because it was < 2 characters long 1081s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '78' because it was < 2 characters long 1081s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '79' because it was < 2 characters long 1081s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '80' because it was < 2 characters long 1081s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '81' because it was < 2 characters long 1081s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '83' because it was < 2 characters long 1081s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '90' because it was < 2 characters long 1081s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '94' because it was < 2 characters long 1081s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '96' because it was < 2 characters long 1081s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '97' because it was < 2 characters long 1081s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '99' because it was < 2 characters long 1081s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '100' because it was < 2 characters long 1081s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '103' because it was < 2 characters long 1081s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '104' because it was < 2 characters long 1081s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '105' because it was < 2 characters long 1081s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '107' because it was < 2 characters long 1081s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '108' because it was < 2 characters long 1081s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '109' because it was < 2 characters long 1081s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '111' because it was < 2 characters long 1081s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '112' because it was < 2 characters long 1081s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '113' because it was < 2 characters long 1081s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '114' because it was < 2 characters long 1081s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '117' because it was < 2 characters long 1081s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '120' because it was < 2 characters long 1081s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '124' because it was < 2 characters long 1081s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '125' because it was < 2 characters long 1081s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '126' because it was < 2 characters long 1081s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '127' because it was < 2 characters long 1081s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '128' because it was < 2 characters long 1081s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '129' because it was < 2 characters long 1081s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '130' because it was < 2 characters long 1081s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '133' because it was < 2 characters long 1081s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '135' because it was < 2 characters long 1081s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '136' because it was < 2 characters long 1081s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '137' because it was < 2 characters long 1081s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '138' because it was < 2 characters long 1081s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '142' because it was < 2 characters long 1081s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '144' because it was < 2 characters long 1081s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '145' because it was < 2 characters long 1081s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '146' because it was < 2 characters long 1081s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '147' because it was < 2 characters long 1081s Warning: skipping read '148' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '148' because it was < 2 characters long 1081s Warning: skipping read '150' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '150' because it was < 2 characters long 1081s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '152' because it was < 2 characters long 1081s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '153' because it was < 2 characters long 1081s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '154' because it was < 2 characters long 1081s Warning: skipping read '155' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '155' because it was < 2 characters long 1081s Warning: skipping read '157' because length (0) <= # seed mismatches (0) 1081s Warning: skipping read '157' because it was < 2 characters long 1081s 157 reads; of these: 1081s 157 (100.00%) were unpaired; of these: 1081s 157 (100.00%) aligned 0 times 1081s 0 (0.00%) aligned exactly 1 time 1081s 0 (0.00%) aligned >1 times 1081s 0.00% overall alignment rate 1081s Read 50 alignments... 1081s Read 100 alignments... 1081s Read 150 alignments... 1081s /usr/bin/bowtie2 --score-min L,4.47888362673349,1.39191741464333 --n-ceil 1.02585625657708,0.266162230690843 --local --trim3 7 -a --trim5 7 --cp-ival 1 --mm --nofw --np 5 --cp-min 7 -f -p 3 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s Processing line... 1081s --- Summary --- 1081s Read 1 reference strings 1081s Checked 0 alignments, 0 edits 1081s --------------- 1081s PASSED 1081s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1082s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '2' because it was < 2 characters long 1082s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '3' because it was < 2 characters long 1082s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '5' because it was < 2 characters long 1082s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '8' because it was < 2 characters long 1082s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '10' because it was < 2 characters long 1082s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '11' because it was < 2 characters long 1082s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '14' because it was < 2 characters long 1082s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '15' because it was < 2 characters long 1082s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '19' because it was < 2 characters long 1082s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '20' because it was < 2 characters long 1082s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '22' because it was < 2 characters long 1082s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '23' because it was < 2 characters long 1082s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '26' because it was < 2 characters long 1082s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '30' because it was < 2 characters long 1082s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '33' because it was < 2 characters long 1082s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '34' because it was < 2 characters long 1082s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '35' because it was < 2 characters long 1082s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '36' because it was < 2 characters long 1082s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 1082s Warning: skipping read '37' because it was < 2 characters long 1082s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '38' because it was < 2 characters long 1082s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '39' because it was < 2 characters long 1082s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '40' because it was < 2 characters long 1082s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '56' because it was < 2 characters long 1082s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '57' because it was < 2 characters long 1082s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '60' because it was < 2 characters long 1082s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '61' because it was < 2 characters long 1082s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '66' because it was < 2 characters long 1082s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '67' because it was < 2 characters long 1082s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '68' because it was < 2 characters long 1082s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '69' because it was < 2 characters long 1082s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '72' because it was < 2 characters long 1082s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '73' because it was < 2 characters long 1082s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '81' because it was < 2 characters long 1082s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '83' because it was < 2 characters long 1082s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '90' because it was < 2 characters long 1082s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '94' because it was < 2 characters long 1082s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '96' because it was < 2 characters long 1082s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '97' because it was < 2 characters long 1082s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '99' because it was < 2 characters long 1082s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '100' because it was < 2 characters long 1082s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '113' because it was < 2 characters long 1082s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '114' because it was < 2 characters long 1082s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '117' because it was < 2 characters long 1082s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '120' because it was < 2 characters long 1082s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '124' because it was < 2 characters long 1082s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '125' because it was < 2 characters long 1082s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '126' because it was < 2 characters long 1082s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '127' because it was < 2 characters long 1082s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '128' because it was < 2 characters long 1082s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '129' because it was < 2 characters long 1082s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '130' because it was < 2 characters long 1082s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '133' because it was < 2 characters long 1082s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '78' because it was < 2 characters long 1082s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '79' because it was < 2 characters long 1082s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '80' because it was < 2 characters long 1082s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '145' because it was < 2 characters long 1082s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '146' because it was < 2 characters long 1082s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '147' because it was < 2 characters long 1082s Warning: skipping read '148' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '148' because it was < 2 characters long 1082s Warning: skipping read '150' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '150' because it was < 2 characters long 1082s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '152' because it was < 2 characters long 1082s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '153' because it was < 2 characters long 1082s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '154' because it was < 2 characters long 1082s Warning: skipping read '155' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '155' because it was < 2 characters long 1082s Warning: skipping read '157' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '157' because it was < 2 characters long 1082s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '135' because it was < 2 characters long 1082s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '136' because it was < 2 characters long 1082s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '137' because it was < 2 characters long 1082s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '138' because it was < 2 characters long 1082s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '142' because it was < 2 characters long 1082s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '144' because it was < 2 characters long 1082s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '103' because it was < 2 characters long 1082s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '104' because it was < 2 characters long 1082s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '105' because it was < 2 characters long 1082s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '107' because it was < 2 characters long 1082s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '108' because it was < 2 characters long 1082s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '109' because it was < 2 characters long 1082s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '111' because it was < 2 characters long 1082s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 1082s Warning: skipping read '112' because it was < 2 characters long 1082s 157 reads; of these: 1082s 157 (100.00%) were unpaired; of these: 1082s 157 (100.00%) aligned 0 times 1082s 0 (0.00%) aligned exactly 1 time 1082s 0 (0.00%) aligned >1 times 1082s 0.00% overall alignment rate 1082s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1082s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1082s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1082s Flattened IUPAC characters 1082s Mutating sequence Sim.pm.2 1082s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1082s Finished SNPs 1082s Finished ref gaps 1082s Finished read gaps 1082s Mutating sequence Sim.pm.1 1082s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1082s Finished SNPs 1082s Finished ref gaps 1082s Finished read gaps 1082s Mutated reference genome to subject genome 1082s SNPs introduced: 5 1082s Reference gaps introduced: 1 1082s Read gaps introduced: 0 1082s Rearrangements introduced: 0 1082s Created read sampler 1082s Sampling 135 reads 1082s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1082s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1082s parsing sequence Sim.pm.1... 1082s parsing sequence Sim.pm.2... 1082s Parsed 7 reference bases 1082s *** Run 46 of 100 1082s /usr/bin/bowtie2 --cp-min 6 --cp-ival 1 --mm --local -a --mp 9.62415020403116,2.82881178494962 --np 1 -R 2 -N 1 -L19 --trim5 7 --score-min L,2.22199120738974,7.09511731429257 --gbar 2 --n-ceil 0.0960730315028726,0.727143671273818 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1082s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1082s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1082s Read 50 alignments... 1082s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1082s Read 100 alignments... 1082s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1082s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (1) 1082s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 1082s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because length (1) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 1082s Warning: skipping read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 1082s Read 150 alignments... 1082s Read 200 alignments... 1082s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because length (1) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 1082s 135 reads; of these: 1082s 116 (85.93%) were paired; of these: 1082s 116 (100.00%) aligned concordantly 0 times 1082s 0 (0.00%) aligned concordantly exactly 1 time 1082s 0 (0.00%) aligned concordantly >1 times 1082s ---- 1082s 116 pairs aligned concordantly 0 times; of these: 1082s 0 (0.00%) aligned discordantly 1 time 1082s ---- 1082s 116 pairs aligned 0 times concordantly or discordantly; of these: 1082s 232 mates make up the pairs; of these: 1082s 232 (100.00%) aligned 0 times 1082s 0 (0.00%) aligned exactly 1 time 1082s 0 (0.00%) aligned >1 times 1082s 19 (14.07%) were unpaired; of these: 1082s 19 (100.00%) aligned 0 times 1082s 0 (0.00%) aligned exactly 1 time 1082s 0 (0.00%) aligned >1 times 1082s 0.00% overall alignment rate 1082s Read 250 alignments... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s Processing line... 1082s 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Read 1 reference strings 1082s Checked 0 alignments, 0 edits 1082s --------------- 1082s PASSED 1082s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1082s /usr/bin/bowtie2 --cp-min 6 --cp-ival 1 --mm --local -a --mp 9.62415020403116,2.82881178494962 --np 1 -R 2 -N 1 -L19 --trim5 7 --score-min L,2.22199120738974,7.09511731429257 --gbar 2 --n-ceil 0.0960730315028726,0.727143671273818 --qseq -p 2 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1082s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1082s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (1) 1082s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1083s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because length (1) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1083s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (1) 1083s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 1083s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 1083s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because length (1) <= # seed mismatches (1) 1083s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 1083s Warning: skipping read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (1) 1083s Warning: skipping read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 1083s 135 reads; of these: 1083s 116 (85.93%) were paired; of these: 1083s 116 (100.00%) aligned concordantly 0 times 1083s 0 (0.00%) aligned concordantly exactly 1 time 1083s 0 (0.00%) aligned concordantly >1 times 1083s ---- 1083s 116 pairs aligned concordantly 0 times; of these: 1083s 0 (0.00%) aligned discordantly 1 time 1083s ---- 1083s 116 pairs aligned 0 times concordantly or discordantly; of these: 1083s 232 mates make up the pairs; of these: 1083s 232 (100.00%) aligned 0 times 1083s 0 (0.00%) aligned exactly 1 time 1083s 0 (0.00%) aligned >1 times 1083s 19 (14.07%) were unpaired; of these: 1083s 19 (100.00%) aligned 0 times 1083s 0 (0.00%) aligned exactly 1 time 1083s 0 (0.00%) aligned >1 times 1083s 0.00% overall alignment rate 1083s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1083s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1083s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1083s Flattened IUPAC characters 1083s Mutating sequence Sim.pm.1 1083s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1083s Finished SNPs 1083s Finished ref gaps 1083s Finished read gaps 1083s Mutating sequence Sim.pm.2 1083s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1083s Finished SNPs 1083s Finished ref gaps 1083s Finished read gaps 1083s Mutated reference genome to subject genome 1083s SNPs introduced: 6 1083s Reference gaps introduced: 0 1083s Read gaps introduced: 0 1083s Rearrangements introduced: 0 1083s Created read sampler 1083s Sampling 81 reads 1083s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1083s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1083s parsing sequence Sim.pm.1... 1083s parsing sequence Sim.pm.2... 1083s Parsed 7 reference bases 1083s *** Run 47 of 100 1083s /usr/bin/bowtie2 --cp-min 5 --np 1 -N 0 -L20 --cp-ival 1 --rdg 17.7646049414721,7.95157520048502 --trim3 9 --mp 1.6189538271218,1.21398245691718 -k 4 --score-min L,7.29505675941698,8.86984499261567 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1083s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '12' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1083s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '13' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1083s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '15' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1083s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '16' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1083s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '17' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1083s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '19' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1083s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '22' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1083s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '25' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1083s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '32' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1083s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '35' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1083s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '36' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1083s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '37' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1083s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '39' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1083s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '47' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1083s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '51' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1083s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '52' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1083s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '53' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1083s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '54' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1083s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '58' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1083s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '61' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1083s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '63' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1083s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '66' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1083s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '71' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1083s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '72' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1083s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '73' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1083s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '75' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1083s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '78' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1083s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '80' because it was < 2 characters long 1083s 81 reads; of these: 1083s 81 (100.00%) were unpaired; of these: 1083s 79 (97.53%) aligned 0 times 1083s 2 (2.47%) aligned exactly 1 time 1083s 0 (0.00%) aligned >1 times 1083s 2.47% overall alignment rate 1083s Read 50 alignments... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s GG 1083s GG 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s GAG 1083s GAG 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s Processing line... 1083s --- Summary --- 1083s Read 1 reference strings 1083s Checked 2 alignments, 0 edits 1083s --------------- 1083s PASSED 1083s ALSO checking that bowtie2 and bowtie2-align match up 1083s /usr/bin/bowtie2 --cp-min 5 --np 1 -N 0 -L20 --cp-ival 1 --rdg 17.7646049414721,7.95157520048502 --trim3 9 --mp 1.6189538271218,1.21398245691718 -k 4 --score-min L,7.29505675941698,8.86984499261567 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1083s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '12' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1083s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '13' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1083s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '15' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1083s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '16' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1083s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '17' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1083s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '19' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1083s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '22' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1083s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '25' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1083s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '32' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1083s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '35' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1083s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '36' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1083s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '37' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1083s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '39' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1083s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '47' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1083s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '51' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1083s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '52' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1083s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '53' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1083s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '54' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1083s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '58' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1083s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '61' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1083s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '63' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1083s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '66' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1083s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '71' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1083s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '72' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1083s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '73' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1083s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '75' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1083s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '78' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1083s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '80' because it was < 2 characters long 1083s 81 reads; of these: 1083s 81 (100.00%) were unpaired; of these: 1083s 79 (97.53%) aligned 0 times 1083s 2 (2.47%) aligned exactly 1 time 1083s 0 (0.00%) aligned >1 times 1083s 2.47% overall alignment rate 1083s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1083s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1083s /usr/bin/bowtie2 --cp-min 5 --np 1 -N 0 -L20 --cp-ival 1 --rdg 17.7646049414721,7.95157520048502 --trim3 9 --mp 1.6189538271218,1.21398245691718 -k 4 --score-min L,7.29505675941698,8.86984499261567 -r -p 4 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1083s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '16' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1083s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '17' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1083s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '19' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1083s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '12' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1083s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '13' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1083s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '15' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1083s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '32' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1083s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '35' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1083s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '36' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1083s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '37' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1083s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '39' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1083s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '47' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1083s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '51' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1083s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '52' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1083s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '53' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1083s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '54' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1083s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '66' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1083s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '71' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1083s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '72' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1083s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '73' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1083s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '75' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1083s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '22' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1083s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '25' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1083s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '58' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1083s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '61' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1083s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '63' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1083s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '80' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1083s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1083s Warning: skipping read '78' because it was < 2 characters long 1083s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1083s 81 reads; of these: 1083s 81 (100.00%) were unpaired; of these: 1083s 79 (97.53%) aligned 0 times 1083s 2 (2.47%) aligned exactly 1 time 1083s 0 (0.00%) aligned >1 times 1083s 2.47% overall alignment rate 1083s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1083s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1083s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1083s Flattened IUPAC characters 1083s Mutating sequence Sim.pm.1 1083s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1083s Finished SNPs 1083s Finished ref gaps 1083s Finished read gaps 1083s Mutating sequence Sim.pm.2 1083s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1083s Finished SNPs 1083s Finished ref gaps 1083s Finished read gaps 1083s Mutated reference genome to subject genome 1083s SNPs introduced: 2 1083s Reference gaps introduced: 1 1083s Read gaps introduced: 0 1083s Rearrangements introduced: 1 1083s Created read sampler 1083s Sampling 18 reads 1084s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1084s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1084s parsing sequence Sim.pm.1... 1084s parsing sequence Sim.pm.2... 1084s Parsed 7 reference bases 1084s *** Run 48 of 100 1084s /usr/bin/bowtie2 --rfg 29.4413863068995 --trim5 3 --score-min L,5.53102079831845,4.9708154562485 --n-ceil 0.951217485290713,0.0877641609217756 --cp-min 7 --cp-ival 2 --mm --local --trim3 6 --rdg 23.1534848823427 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1084s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1084s Warning: skipping read '3' because it was < 2 characters long 1084s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1084s Warning: skipping read '8' because it was < 2 characters long 1084s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 1084s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1084s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1084s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1084s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1084s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1084s 18 reads; of these: 1084s 14 (77.78%) were paired; of these: 1084s 14 (100.00%) aligned concordantly 0 times 1084s 0 (0.00%) aligned concordantly exactly 1 time 1084s 0 (0.00%) aligned concordantly >1 times 1084s ---- 1084s 14 pairs aligned concordantly 0 times; of these: 1084s 0 (0.00%) aligned discordantly 1 time 1084s ---- 1084s 14 pairs aligned 0 times concordantly or discordantly; of these: 1084s 28 mates make up the pairs; of these: 1084s 28 (100.00%) aligned 0 times 1084s 0 (0.00%) aligned exactly 1 time 1084s 0 (0.00%) aligned >1 times 1084s 4 (22.22%) were unpaired; of these: 1084s 4 (100.00%) aligned 0 times 1084s 0 (0.00%) aligned exactly 1 time 1084s 0 (0.00%) aligned >1 times 1084s 0.00% overall alignment rate 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s /usr/bin/bowtie2 --rfg 29.4413863068995 --trim5 3 --score-min L,5.53102079831845,4.9708154562485 --n-ceil 0.951217485290713,0.0877641609217756 --cp-min 7 --cp-ival 2 --mm --local --trim3 6 --rdg 23.1534848823427 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s Processing line... 1084s --- Summary --- 1084s Read 1 reference strings 1084s Checked 0 alignments, 0 edits 1084s --------------- 1084s PASSED 1084s ALSO checking that bowtie2 and bowtie2-align match up 1084s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1084s Warning: skipping read '3' because it was < 2 characters long 1084s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1084s Warning: skipping read '8' because it was < 2 characters long 1084s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 1084s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1084s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1084s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1084s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1084s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1084s 18 reads; of these: 1084s 14 (77.78%) were paired; of these: 1084s 14 (100.00%) aligned concordantly 0 times 1084s 0 (0.00%) aligned concordantly exactly 1 time 1084s 0 (0.00%) aligned concordantly >1 times 1084s ---- 1084s 14 pairs aligned concordantly 0 times; of these: 1084s 0 (0.00%) aligned discordantly 1 time 1084s ---- 1084s 14 pairs aligned 0 times concordantly or discordantly; of these: 1084s 28 mates make up the pairs; of these: 1084s 28 (100.00%) aligned 0 times 1084s 0 (0.00%) aligned exactly 1 time 1084s 0 (0.00%) aligned >1 times 1084s 4 (22.22%) were unpaired; of these: 1084s 4 (100.00%) aligned 0 times 1084s 0 (0.00%) aligned exactly 1 time 1084s 0 (0.00%) aligned >1 times 1084s 0.00% overall alignment rate 1084s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1084s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1084s /usr/bin/bowtie2 --rfg 29.4413863068995 --trim5 3 --score-min L,5.53102079831845,4.9708154562485 --n-ceil 0.951217485290713,0.0877641609217756 --cp-min 7 --cp-ival 2 --mm --local --trim3 6 --rdg 23.1534848823427 -f -p 4 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1084s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1084s Warning: skipping read '3' because it was < 2 characters long 1084s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1084s Warning: skipping read '8' because it was < 2 characters long 1084s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 1084s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1084s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1084s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1084s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1084s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1084s 18 reads; of these: 1084s 14 (77.78%) were paired; of these: 1084s 14 (100.00%) aligned concordantly 0 times 1084s 0 (0.00%) aligned concordantly exactly 1 time 1084s 0 (0.00%) aligned concordantly >1 times 1084s ---- 1084s 14 pairs aligned concordantly 0 times; of these: 1084s 0 (0.00%) aligned discordantly 1 time 1084s ---- 1084s 14 pairs aligned 0 times concordantly or discordantly; of these: 1084s 28 mates make up the pairs; of these: 1084s 28 (100.00%) aligned 0 times 1084s 0 (0.00%) aligned exactly 1 time 1084s 0 (0.00%) aligned >1 times 1084s 4 (22.22%) were unpaired; of these: 1084s 4 (100.00%) aligned 0 times 1084s 0 (0.00%) aligned exactly 1 time 1084s 0 (0.00%) aligned >1 times 1084s 0.00% overall alignment rate 1084s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1084s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1084s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1084s Flattened IUPAC characters 1084s Mutating sequence Sim.pm.1 1084s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1084s Finished SNPs 1084s Finished ref gaps 1084s Finished read gaps 1084s Mutating sequence Sim.pm.2 1084s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1084s Finished SNPs 1084s Finished ref gaps 1084s Finished read gaps 1084s Mutated reference genome to subject genome 1084s SNPs introduced: 7 1084s Reference gaps introduced: 1 1084s Read gaps introduced: 0 1084s Rearrangements introduced: 1 1084s Created read sampler 1084s Sampling 34 reads 1084s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1084s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1084s parsing sequence Sim.pm.1... 1084s parsing sequence Sim.pm.2... 1084s Parsed 7 reference bases 1084s *** Run 49 of 100 1084s /usr/bin/bowtie2 --trim5 4 --local --n-ceil 1.02664353175308,0.771237864883253 --score-min L,8.885078574173,2.97233737755971 --cp-min 2 --np 4 --cp-ival 1 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1085s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 1085s Warning: skipping mate #2 of read '7' because it was < 2 characters long 1085s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1085s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1085s 34 reads; of these: 1085s 34 (100.00%) were paired; of these: 1085s 34 (100.00%) aligned concordantly 0 times 1085s 0 (0.00%) aligned concordantly exactly 1 time 1085s 0 (0.00%) aligned concordantly >1 times 1085s ---- 1085s 34 pairs aligned concordantly 0 times; of these: 1085s 0 (0.00%) aligned discordantly 1 time 1085s ---- 1085s 34 pairs aligned 0 times concordantly or discordantly; of these: 1085s 68 mates make up the pairs; of these: 1085s 68 (100.00%) aligned 0 times 1085s 0 (0.00%) aligned exactly 1 time 1085s 0 (0.00%) aligned >1 times 1085s 0.00% overall alignment rate 1085s Read 50 alignments... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s --- Summary --- 1085s Read 1 reference strings 1085s Checked 0 alignments, 0 edits 1085s --------------- 1085s PASSED 1085s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1085s /usr/bin/bowtie2 --trim5 4 --local --n-ceil 1.02664353175308,0.771237864883253 --score-min L,8.885078574173,2.97233737755971 --cp-min 2 --np 4 --cp-ival 1 -f -p 2 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1085s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 1085s Warning: skipping mate #2 of read '7' because it was < 2 characters long 1085s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1085s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1085s 34 reads; of these: 1085s 34 (100.00%) were paired; of these: 1085s 34 (100.00%) aligned concordantly 0 times 1085s 0 (0.00%) aligned concordantly exactly 1 time 1085s 0 (0.00%) aligned concordantly >1 times 1085s ---- 1085s 34 pairs aligned concordantly 0 times; of these: 1085s 0 (0.00%) aligned discordantly 1 time 1085s ---- 1085s 34 pairs aligned 0 times concordantly or discordantly; of these: 1085s 68 mates make up the pairs; of these: 1085s 68 (100.00%) aligned 0 times 1085s 0 (0.00%) aligned exactly 1 time 1085s 0 (0.00%) aligned >1 times 1085s 0.00% overall alignment rate 1085s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1085s Flattened IUPAC characters 1085s Mutating sequence Sim.pm.2 1085s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1085s Finished SNPs 1085s Finished ref gaps 1085s Finished read gaps 1085s Mutating sequence Sim.pm.1 1085s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1085s Finished SNPs 1085s Finished ref gaps 1085s Finished read gaps 1085s Mutated reference genome to subject genome 1085s SNPs introduced: 5 1085s Reference gaps introduced: 1 1085s Read gaps introduced: 0 1085s Rearrangements introduced: 0 1085s Created read sampler 1085s Sampling 106 reads 1085s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1085s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1085s parsing sequence Sim.pm.1... 1085s parsing sequence Sim.pm.2... 1085s Parsed 7 reference bases 1085s *** Run 50 of 100 1085s /usr/bin/bowtie2 --cp-ival 3 --cp-min 2 --ma 30.7258653294754 --n-ceil 0.24081552283341,0.997840940634013 -k 6 --score-min L,3.9973732651103,3.99769082190642 --rdg 32.9863798757281 --trim5 9 --rfg 32.7372194145171,4.13966539263332 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1085s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 1085s 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 1085s 106 reads; of these: 1085s 106 (100.00%) were unpaired; of these: 1085s 103 (97.17%) aligned 0 times 1085s 3 (2.83%) aligned exactly 1 time 1085s 0 (0.00%) aligned >1 times 1085s 2.83% overall alignment rate 1085s Read 50 alignments... 1085s Read 100 alignments... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s AG 1085s AG 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s GG 1085s GG 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s GG 1085s GG 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s Processing line... 1085s --- Summary --- 1085s Read 1 reference strings 1085s Checked 3 alignments, 0 edits 1085s --------------- 1085s PASSED 1085s ALSO checking that bowtie2 and bowtie2-align match up 1085s /usr/bin/bowtie2 --cp-ival 3 --cp-min 2 --ma 30.7258653294754 --n-ceil 0.24081552283341,0.997840940634013 -k 6 --score-min L,3.9973732651103,3.99769082190642 --rdg 32.9863798757281 --trim5 9 --rfg 32.7372194145171,4.13966539263332 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1085s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s 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 1085s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1085s 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 1085s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 1085s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 1085s 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 1085s 106 reads; of these: 1085s 106 (100.00%) were unpaired; of these: 1085s 103 (97.17%) aligned 0 times 1085s 3 (2.83%) aligned exactly 1 time 1085s 0 (0.00%) aligned >1 times 1085s 2.83% overall alignment rate 1085s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1085s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1085s /usr/bin/bowtie2 --cp-ival 3 --cp-min 2 --ma 30.7258653294754 --n-ceil 0.24081552283341,0.997840940634013 -k 6 --score-min L,3.9973732651103,3.99769082190642 --rdg 32.9863798757281 --trim5 9 --rfg 32.7372194145171,4.13966539263332 --qseq -p 2 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1086s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1086s 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 1086s 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 1086s 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 1086s 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 1086s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1086s 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 1086s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 1086s 106 reads; of these: 1086s 106 (100.00%) were unpaired; of these: 1086s 103 (97.17%) aligned 0 times 1086s 3 (2.83%) aligned exactly 1 time 1086s 0 (0.00%) aligned >1 times 1086s 2.83% overall alignment rate 1086s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1086s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1086s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1086s Flattened IUPAC characters 1086s Mutating sequence Sim.pm.2 1086s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1086s Finished SNPs 1086s Finished ref gaps 1086s Finished read gaps 1086s Mutating sequence Sim.pm.1 1086s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1086s Finished SNPs 1086s Finished ref gaps 1086s Finished read gaps 1086s Mutated reference genome to subject genome 1086s SNPs introduced: 5 1086s Reference gaps introduced: 0 1086s Read gaps introduced: 0 1086s Rearrangements introduced: 0 1086s Created read sampler 1086s Sampling 137 reads 1086s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1086s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1086s parsing sequence Sim.pm.1... 1086s parsing sequence Sim.pm.2... 1086s *** Run 51 of 100 1086s /usr/bin/bowtie2 --trim5 6 --rfg 47.3710102241188 -i L,0.448586282147949 --score-min L,1.06065438741614,3.19630719101341 -R 4 --mp 9.43490235878467,8.35115610288841 --local -M 3 --cp-min 3 --cp-ival 1 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1086s Parsed 7 reference bases 1086s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1086s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1086s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #2 of read '4' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1086s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #2 of read '39' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '54' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1086s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #2 of read '72' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '78' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '80' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '80' because it was < 2 characters long 1086s Read 50 alignments... 1086s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '90' because it was < 2 characters long 1086s Read 100 alignments... 1086s Warning: skipping mate #1 of read '101' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '101' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '113' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '121' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '123' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '124' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '136' because it was < 2 characters long 1086s 137 reads; of these: 1086s 126 (91.97%) were paired; of these: 1086s 126 (100.00%) aligned concordantly 0 times 1086s 0 (0.00%) aligned concordantly exactly 1 time 1086s 0 (0.00%) aligned concordantly >1 times 1086s ---- 1086s 126 pairs aligned concordantly 0 times; of these: 1086s 0 (0.00%) aligned discordantly 1 time 1086s ---- 1086s 126 pairs aligned 0 times concordantly or discordantly; of these: 1086s 252 mates make up the pairs; of these: 1086s 252 (100.00%) aligned 0 times 1086s 0 (0.00%) aligned exactly 1 time 1086s 0 (0.00%) aligned >1 times 1086s 11 (8.03%) were unpaired; of these: 1086s 11 (100.00%) aligned 0 times 1086s 0 (0.00%) aligned exactly 1 time 1086s 0 (0.00%) aligned >1 times 1086s 0.00% overall alignment rate 1086s Read 150 alignments... 1086s Read 200 alignments... 1086s Read 250 alignments... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s 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Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s Processing line... 1086s --- Summary --- 1086s Read 1 reference strings 1086s Checked 0 alignments, 0 edits 1086s /usr/bin/bowtie2 --trim5 6 --rfg 47.3710102241188 -i L,0.448586282147949 --score-min L,1.06065438741614,3.19630719101341 -R 4 --mp 9.43490235878467,8.35115610288841 --local -M 3 --cp-min 3 --cp-ival 1 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1086s --------------- 1086s PASSED 1086s ALSO checking that bowtie2 and bowtie2-align match up 1086s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1086s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1086s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #2 of read '4' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1086s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #2 of read '39' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '54' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1086s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #2 of read '72' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '78' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '80' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '80' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '90' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '101' because length (1) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '101' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '113' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '121' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '123' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '124' because it was < 2 characters long 1086s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 1086s Warning: skipping mate #1 of read '136' because it was < 2 characters long 1086s 137 reads; of these: 1086s 126 (91.97%) were paired; of these: 1086s 126 (100.00%) aligned concordantly 0 times 1086s 0 (0.00%) aligned concordantly exactly 1 time 1086s 0 (0.00%) aligned concordantly >1 times 1086s ---- 1086s 126 pairs aligned concordantly 0 times; of these: 1086s 0 (0.00%) aligned discordantly 1 time 1086s ---- 1086s 126 pairs aligned 0 times concordantly or discordantly; of these: 1086s 252 mates make up the pairs; of these: 1086s 252 (100.00%) aligned 0 times 1086s 0 (0.00%) aligned exactly 1 time 1086s 0 (0.00%) aligned >1 times 1086s 11 (8.03%) were unpaired; of these: 1086s 11 (100.00%) aligned 0 times 1086s 0 (0.00%) aligned exactly 1 time 1086s 0 (0.00%) aligned >1 times 1086s 0.00% overall alignment rate 1086s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1087s Flattened IUPAC characters 1087s Mutating sequence Sim.pm.2 1087s Introducing 5 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1087s Finished SNPs 1087s Finished ref gaps 1087s Finished read gaps 1087s Mutating sequence Sim.pm.1 1087s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1087s Finished SNPs 1087s Finished ref gaps 1087s Finished read gaps 1087s Mutated reference genome to subject genome 1087s SNPs introduced: 8 1087s Reference gaps introduced: 1 1087s Read gaps introduced: 1 1087s Rearrangements introduced: 1 1087s Created read sampler 1087s Sampling 115 reads 1087s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1087s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1087s parsing sequence Sim.pm.1... 1087s parsing sequence Sim.pm.2... 1087s Parsed 7 reference bases 1087s *** Run 52 of 100 1087s /usr/bin/bowtie2 --norc --np 6 --nofw -i S,0.842553578138842 --trim5 3 --score-min L,3.68518558109215,4.53491410355442 --n-ceil 0.437305621882425,0.167290375437439 --cp-min 5 --cp-ival 2 --local --rdg 42.4097503841989 --trim3 9 --mp 4.77569925595747,1.4422675508972 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1087s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1087s Warning: skipping mate #2 of read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 1087s Warning: skipping mate #2 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1087s Read 50 alignments... 1087s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 1087s Read 100 alignments... 1087s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 1087s 115 reads; of these: 1087s 84 (73.04%) were paired; of these: 1087s 84 (100.00%) aligned concordantly 0 times 1087s 0 (0.00%) aligned concordantly exactly 1 time 1087s 0 (0.00%) aligned concordantly >1 times 1087s ---- 1087s 84 pairs aligned concordantly 0 times; of these: 1087s 0 (0.00%) aligned discordantly 1 time 1087s ---- 1087s 84 pairs aligned 0 times concordantly or discordantly; of these: 1087s 168 mates make up the pairs; of these: 1087s 168 (100.00%) aligned 0 times 1087s 0 (0.00%) aligned exactly 1 time 1087s 0 (0.00%) aligned >1 times 1087s 31 (26.96%) were unpaired; of these: 1087s 31 (100.00%) aligned 0 times 1087s 0 (0.00%) aligned exactly 1 time 1087s 0 (0.00%) aligned >1 times 1087s 0.00% overall alignment rate 1087s Read 150 alignments... 1087s Read 200 alignments... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s /usr/bin/bowtie2 --norc --np 6 --nofw -i S,0.842553578138842 --trim5 3 --score-min L,3.68518558109215,4.53491410355442 --n-ceil 0.437305621882425,0.167290375437439 --cp-min 5 --cp-ival 2 --local --rdg 42.4097503841989 --trim3 9 --mp 4.77569925595747,1.4422675508972 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s Processing line... 1087s --- Summary --- 1087s Read 1 reference strings 1087s Checked 0 alignments, 0 edits 1087s --------------- 1087s PASSED 1087s ALSO checking that bowtie2 and bowtie2-align match up 1087s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1087s Warning: skipping mate #2 of read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 1087s Warning: skipping mate #2 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 1087s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 1087s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 1087s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 1087s 115 reads; of these: 1087s 84 (73.04%) were paired; of these: 1087s 84 (100.00%) aligned concordantly 0 times 1087s 0 (0.00%) aligned concordantly exactly 1 time 1087s 0 (0.00%) aligned concordantly >1 times 1087s ---- 1087s 84 pairs aligned concordantly 0 times; of these: 1087s 0 (0.00%) aligned discordantly 1 time 1087s ---- 1087s 84 pairs aligned 0 times concordantly or discordantly; of these: 1087s 168 mates make up the pairs; of these: 1087s 168 (100.00%) aligned 0 times 1087s 0 (0.00%) aligned exactly 1 time 1087s 0 (0.00%) aligned >1 times 1087s 31 (26.96%) were unpaired; of these: 1087s 31 (100.00%) aligned 0 times 1087s 0 (0.00%) aligned exactly 1 time 1087s 0 (0.00%) aligned >1 times 1087s 0.00% overall alignment rate 1087s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1087s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1087s /usr/bin/bowtie2 --norc --np 6 --nofw -i S,0.842553578138842 --trim5 3 --score-min L,3.68518558109215,4.53491410355442 --n-ceil 0.437305621882425,0.167290375437439 --cp-min 5 --cp-ival 2 --local --rdg 42.4097503841989 --trim3 9 --mp 4.77569925595747,1.4422675508972 --qseq -p 2 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1088s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1088s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1088s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1088s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1088s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1088s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1088s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1088s Warning: skipping mate #2 of read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 1088s Warning: skipping mate #2 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1088s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1088s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 1088s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 1088s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1088s 115 reads; of these: 1088s 84 (73.04%) were paired; of these: 1088s 84 (100.00%) aligned concordantly 0 times 1088s 0 (0.00%) aligned concordantly exactly 1 time 1088s 0 (0.00%) aligned concordantly >1 times 1088s ---- 1088s 84 pairs aligned concordantly 0 times; of these: 1088s 0 (0.00%) aligned discordantly 1 time 1088s ---- 1088s 84 pairs aligned 0 times concordantly or discordantly; of these: 1088s 168 mates make up the pairs; of these: 1088s 168 (100.00%) aligned 0 times 1088s 0 (0.00%) aligned exactly 1 time 1088s 0 (0.00%) aligned >1 times 1088s 31 (26.96%) were unpaired; of these: 1088s 31 (100.00%) aligned 0 times 1088s 0 (0.00%) aligned exactly 1 time 1088s 0 (0.00%) aligned >1 times 1088s 0.00% overall alignment rate 1088s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1088s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1088s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1088s Flattened IUPAC characters 1088s Mutating sequence Sim.pm.2 1088s Introducing 2 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1088s Finished SNPs 1088s Finished ref gaps 1088s Finished read gaps 1088s Mutating sequence Sim.pm.1 1088s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1088s Finished SNPs 1088s Finished ref gaps 1088s Finished read gaps 1088s Mutated reference genome to subject genome 1088s SNPs introduced: 9 1088s Reference gaps introduced: 1 1088s Read gaps introduced: 0 1088s Rearrangements introduced: 2 1088s Created read sampler 1088s Sampling 46 reads 1088s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1088s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1088s parsing sequence Sim.pm.1... 1088s parsing sequence Sim.pm.2... 1088s Parsed 7 reference bases 1088s *** Run 53 of 100 1088s /usr/bin/bowtie2 --ma 6.58010450532142 --rdg 2.28563455691512,6.07890267656498 --mp 6.87877850732588,6.15684545195283 --trim3 4 --cp-ival 1 --cp-min 7 --score-min L,7.53005666334872,3.13303741920189 --rfg 26.1520620691242,11.2587095382578 -i S --nofw -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1088s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1088s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1088s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1088s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1088s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1088s 46 reads; of these: 1088s 40 (86.96%) were paired; of these: 1088s 40 (100.00%) aligned concordantly 0 times 1088s 0 (0.00%) aligned concordantly exactly 1 time 1088s 0 (0.00%) aligned concordantly >1 times 1088s ---- 1088s 40 pairs aligned concordantly 0 times; of these: 1088s 0 (0.00%) aligned discordantly 1 time 1088s ---- 1088s 40 pairs aligned 0 times concordantly or discordantly; of these: 1088s 80 mates make up the pairs; of these: 1088s 80 (100.00%) aligned 0 times 1088s 0 (0.00%) aligned exactly 1 time 1088s 0 (0.00%) aligned >1 times 1088s 6 (13.04%) were unpaired; of these: 1088s 6 (100.00%) aligned 0 times 1088s 0 (0.00%) aligned exactly 1 time 1088s 0 (0.00%) aligned >1 times 1088s 0.00% overall alignment rate 1088s Read 50 alignments... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s Processing line... 1088s --- Summary --- 1088s Read 1 reference strings 1088s Checked 0 alignments, 0 edits 1088s --------------- 1088s PASSED 1088s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1088s /usr/bin/bowtie2 --ma 6.58010450532142 --rdg 2.28563455691512,6.07890267656498 --mp 6.87877850732588,6.15684545195283 --trim3 4 --cp-ival 1 --cp-min 7 --score-min L,7.53005666334872,3.13303741920189 --rfg 26.1520620691242,11.2587095382578 -i S --nofw -f -p 2 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1088s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1088s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1088s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1088s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1088s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 1088s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1088s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1088s 46 reads; of these: 1088s 40 (86.96%) were paired; of these: 1088s 40 (100.00%) aligned concordantly 0 times 1088s 0 (0.00%) aligned concordantly exactly 1 time 1088s 0 (0.00%) aligned concordantly >1 times 1088s ---- 1088s 40 pairs aligned concordantly 0 times; of these: 1088s 0 (0.00%) aligned discordantly 1 time 1088s ---- 1088s 40 pairs aligned 0 times concordantly or discordantly; of these: 1088s 80 mates make up the pairs; of these: 1088s 80 (100.00%) aligned 0 times 1088s 0 (0.00%) aligned exactly 1 time 1088s 0 (0.00%) aligned >1 times 1088s 6 (13.04%) were unpaired; of these: 1088s 6 (100.00%) aligned 0 times 1088s 0 (0.00%) aligned exactly 1 time 1088s 0 (0.00%) aligned >1 times 1088s 0.00% overall alignment rate 1088s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1088s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1088s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1088s Flattened IUPAC characters 1088s Mutating sequence Sim.pm.1 1088s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1088s Finished SNPs 1088s Finished ref gaps 1088s Finished read gaps 1088s Mutating sequence Sim.pm.2 1088s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1088s Finished SNPs 1088s Finished ref gaps 1088s Finished read gaps 1088s Mutated reference genome to subject genome 1088s SNPs introduced: 5 1088s Reference gaps introduced: 0 1088s Read gaps introduced: 0 1088s Rearrangements introduced: 1 1088s Created read sampler 1088s Sampling 81 reads 1088s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1088s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1088s parsing sequence Sim.pm.1... 1088s parsing sequence Sim.pm.2... 1088s Parsed 7 reference bases 1088s *** Run 54 of 100 1088s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 2 --local --rdg 44.6681800432481 --mp 5.23889799989123,2.17380123016103 --norc --np 1 --gbar 1 --score-min L,6.14178858606705,3.68270266429974 --rfg 23.5443894985472 --trim5 3 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1089s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '13' because it was < 2 characters long 1089s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '18' because it was < 2 characters long 1089s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 1089s Warning: skipping read '25' because it was < 2 characters long 1089s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '31' because it was < 2 characters long 1089s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '34' because it was < 2 characters long 1089s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '41' because it was < 2 characters long 1089s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '42' because it was < 2 characters long 1089s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '50' because it was < 2 characters long 1089s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '51' because it was < 2 characters long 1089s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1089s Warning: skipping read '52' because it was < 2 characters long 1089s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '56' because it was < 2 characters long 1089s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 1089s Warning: skipping read '59' because it was < 2 characters long 1089s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '69' because it was < 2 characters long 1089s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '71' because it was < 2 characters long 1089s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '72' because it was < 2 characters long 1089s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '75' because it was < 2 characters long 1089s 81 reads; of these: 1089s 81 (100.00%) were unpaired; of these: 1089s 81 (100.00%) aligned 0 times 1089s 0 (0.00%) aligned exactly 1 time 1089s 0 (0.00%) aligned >1 times 1089s 0.00% overall alignment rate 1089s Read 50 alignments... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s --- Summary --- 1089s Read 1 reference strings 1089s Checked 0 alignments, 0 edits 1089s --------------- 1089s PASSED 1089s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1089s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 2 --local --rdg 44.6681800432481 --mp 5.23889799989123,2.17380123016103 --norc --np 1 --gbar 1 --score-min L,6.14178858606705,3.68270266429974 --rfg 23.5443894985472 --trim5 3 -r -p 3 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1089s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '13' because it was < 2 characters long 1089s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '18' because it was < 2 characters long 1089s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 1089s Warning: skipping read '25' because it was < 2 characters long 1089s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '31' because it was < 2 characters long 1089s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '34' because it was < 2 characters long 1089s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '41' because it was < 2 characters long 1089s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '42' because it was < 2 characters long 1089s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '50' because it was < 2 characters long 1089s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '51' because it was < 2 characters long 1089s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1089s Warning: skipping read '52' because it was < 2 characters long 1089s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '56' because it was < 2 characters long 1089s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 1089s Warning: skipping read '59' because it was < 2 characters long 1089s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '69' because it was < 2 characters long 1089s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '71' because it was < 2 characters long 1089s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '72' because it was < 2 characters long 1089s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1089s Warning: skipping read '75' because it was < 2 characters long 1089s 81 reads; of these: 1089s 81 (100.00%) were unpaired; of these: 1089s 81 (100.00%) aligned 0 times 1089s 0 (0.00%) aligned exactly 1 time 1089s 0 (0.00%) aligned >1 times 1089s 0.00% overall alignment rate 1089s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1089s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1089s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1089s Flattened IUPAC characters 1089s Mutating sequence Sim.pm.2 1089s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1089s Finished SNPs 1089s Finished ref gaps 1089s Finished read gaps 1089s Mutating sequence Sim.pm.1 1089s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1089s Finished SNPs 1089s Finished ref gaps 1089s Finished read gaps 1089s Mutated reference genome to subject genome 1089s SNPs introduced: 3 1089s Reference gaps introduced: 1 1089s Read gaps introduced: 0 1089s Rearrangements introduced: 0 1089s Created read sampler 1089s Sampling 107 reads 1089s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1089s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1089s parsing sequence Sim.pm.1... 1089s parsing sequence Sim.pm.2... 1089s Parsed 7 reference bases 1089s *** Run 55 of 100 1089s /usr/bin/bowtie2 --local --rdg 46.0082594587943 --trim3 3 --cp-min 3 --mm --cp-ival 1 --rfg 9.34745274229603,6.60881349432708 --gbar 1 --score-min L,9.37343342217703,7.68292420592558 -D 44 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1089s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 1089s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1089s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1089s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1089s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1089s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1089s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 1089s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1089s Read 50 alignments... 1089s Read 100 alignments... 1089s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1089s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1089s Warning: skipping mate #2 of read 'R_1_1_1_107_107_1/1' because length (1) <= # seed mismatches (0) 1089s Warning: skipping mate #2 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 1089s 107 reads; of these: 1089s 96 (89.72%) were paired; of these: 1089s 96 (100.00%) aligned concordantly 0 times 1089s 0 (0.00%) aligned concordantly exactly 1 time 1089s 0 (0.00%) aligned concordantly >1 times 1089s ---- 1089s 96 pairs aligned concordantly 0 times; of these: 1089s 0 (0.00%) aligned discordantly 1 time 1089s ---- 1089s 96 pairs aligned 0 times concordantly or discordantly; of these: 1089s 192 mates make up the pairs; of these: 1089s 192 (100.00%) aligned 0 times 1089s 0 (0.00%) aligned exactly 1 time 1089s 0 (0.00%) aligned >1 times 1089s 11 (10.28%) were unpaired; of these: 1089s 11 (100.00%) aligned 0 times 1089s 0 (0.00%) aligned exactly 1 time 1089s 0 (0.00%) aligned >1 times 1089s 0.00% overall alignment rate 1089s Read 150 alignments... 1089s Read 200 alignments... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 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1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s Processing line... 1089s --- Summary --- 1089s Read 1 reference strings 1089s Checked 0 alignments, 0 edits 1089s --------------- 1089s PASSED 1089s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1089s /usr/bin/bowtie2 --local --rdg 46.0082594587943 --trim3 3 --cp-min 3 --mm --cp-ival 1 --rfg 9.34745274229603,6.60881349432708 --gbar 1 --score-min L,9.37343342217703,7.68292420592558 -D 44 --qseq -p 4 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1090s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 1090s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1090s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 1090s Warning: skipping mate #2 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1090s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1090s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1090s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1090s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1090s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1090s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1090s Warning: skipping mate #2 of read 'R_1_1_1_107_107_1/1' because length (1) <= # seed mismatches (0) 1090s Warning: skipping mate #2 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 1090s 107 reads; of these: 1090s 96 (89.72%) were paired; of these: 1090s 96 (100.00%) aligned concordantly 0 times 1090s 0 (0.00%) aligned concordantly exactly 1 time 1090s 0 (0.00%) aligned concordantly >1 times 1090s ---- 1090s 96 pairs aligned concordantly 0 times; of these: 1090s 0 (0.00%) aligned discordantly 1 time 1090s ---- 1090s 96 pairs aligned 0 times concordantly or discordantly; of these: 1090s 192 mates make up the pairs; of these: 1090s 192 (100.00%) aligned 0 times 1090s 0 (0.00%) aligned exactly 1 time 1090s 0 (0.00%) aligned >1 times 1090s 11 (10.28%) were unpaired; of these: 1090s 11 (100.00%) aligned 0 times 1090s 0 (0.00%) aligned exactly 1 time 1090s 0 (0.00%) aligned >1 times 1090s 0.00% overall alignment rate 1090s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1090s Flattened IUPAC characters 1090s Mutating sequence Sim.pm.1 1090s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1090s Finished SNPs 1090s Finished ref gaps 1090s Finished read gaps 1090s Mutating sequence Sim.pm.2 1090s Introducing 2 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1090s Finished SNPs 1090s Finished ref gaps 1090s Finished read gaps 1090s Mutated reference genome to subject genome 1090s SNPs introduced: 7 1090s Reference gaps introduced: 1 1090s Read gaps introduced: 1 1090s Rearrangements introduced: 0 1090s Created read sampler 1090s Sampling 46 reads 1090s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1090s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1090s parsing sequence Sim.pm.1... 1090s parsing sequence Sim.pm.2... 1090s Parsed 7 reference bases 1090s *** Run 56 of 100 1090s /usr/bin/bowtie2 -k 7 --score-min L,4.87739109926775,4.04889794492923 --trim3 7 --mp 8.13386429444815,7.05412305034719 --local --rfg 4.80280148388731 -N 1 --cp-ival 1 --cp-min 2 --norc --np 5 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1090s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1090s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (1) 1090s Warning: skipping mate #2 of read '7' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1090s Warning: skipping read '23' because length (1) <= # seed mismatches (1) 1090s Warning: skipping read '23' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '26' because length (1) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1090s 46 reads; of these: 1090s 40 (86.96%) were paired; of these: 1090s 40 (100.00%) aligned concordantly 0 times 1090s 0 (0.00%) aligned concordantly exactly 1 time 1090s 0 (0.00%) aligned concordantly >1 times 1090s ---- 1090s 40 pairs aligned concordantly 0 times; of these: 1090s 0 (0.00%) aligned discordantly 1 time 1090s ---- 1090s 40 pairs aligned 0 times concordantly or discordantly; of these: 1090s 80 mates make up the pairs; of these: 1090s 80 (100.00%) aligned 0 times 1090s 0 (0.00%) aligned exactly 1 time 1090s 0 (0.00%) aligned >1 times 1090s 6 (13.04%) were unpaired; of these: 1090s 6 (100.00%) aligned 0 times 1090s 0 (0.00%) aligned exactly 1 time 1090s 0 (0.00%) aligned >1 times 1090s 0.00% overall alignment rate 1090s Read 50 alignments... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s Processing line... 1090s --- Summary --- 1090s Read 1 reference strings 1090s Checked 0 alignments, 0 edits 1090s --------------- 1090s PASSED 1090s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1090s /usr/bin/bowtie2 -k 7 --score-min L,4.87739109926775,4.04889794492923 --trim3 7 --mp 8.13386429444815,7.05412305034719 --local --rfg 4.80280148388731 -N 1 --cp-ival 1 --cp-min 2 --norc --np 5 -q -p 2 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1090s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1090s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (1) 1090s Warning: skipping mate #2 of read '7' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1090s Warning: skipping read '23' because length (1) <= # seed mismatches (1) 1090s Warning: skipping read '23' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '26' because length (1) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1090s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (1) 1090s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1090s 46 reads; of these: 1090s 40 (86.96%) were paired; of these: 1090s 40 (100.00%) aligned concordantly 0 times 1090s 0 (0.00%) aligned concordantly exactly 1 time 1090s 0 (0.00%) aligned concordantly >1 times 1090s ---- 1090s 40 pairs aligned concordantly 0 times; of these: 1090s 0 (0.00%) aligned discordantly 1 time 1090s ---- 1090s 40 pairs aligned 0 times concordantly or discordantly; of these: 1090s 80 mates make up the pairs; of these: 1090s 80 (100.00%) aligned 0 times 1090s 0 (0.00%) aligned exactly 1 time 1090s 0 (0.00%) aligned >1 times 1090s 6 (13.04%) were unpaired; of these: 1090s 6 (100.00%) aligned 0 times 1090s 0 (0.00%) aligned exactly 1 time 1090s 0 (0.00%) aligned >1 times 1090s 0.00% overall alignment rate 1090s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1090s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1090s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1090s Flattened IUPAC characters 1090s Mutating sequence Sim.pm.1 1090s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1090s Finished SNPs 1090s Finished ref gaps 1090s Finished read gaps 1090s Mutating sequence Sim.pm.2 1090s Introducing 4 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1090s Finished SNPs 1090s Finished ref gaps 1090s Finished read gaps 1090s Mutated reference genome to subject genome 1090s SNPs introduced: 6 1090s Reference gaps introduced: 1 1090s Read gaps introduced: 1 1090s Rearrangements introduced: 0 1090s Created read sampler 1090s Sampling 72 reads 1090s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1090s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1090s parsing sequence Sim.pm.1... 1090s parsing sequence Sim.pm.2... 1090s *** Run 57 of 100 1090s /usr/bin/bowtie2 --cp-min 5 --cp-ival 1 --mm --ma 8.97985814245788 -k 2 --np 5 --norc -R 3 --rfg 39.0503761229487 --score-min L,6.04579285806622,9.0245041461116 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1090s Parsed 7 reference bases 1091s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1091s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #2 of read '11' because it was < 2 characters long 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1091s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1091s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #2 of read '57' because it was < 2 characters long 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1091s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1091s 72 reads; of these: 1091s 72 (100.00%) were paired; of these: 1091s 72 (100.00%) aligned concordantly 0 times 1091s 0 (0.00%) aligned concordantly exactly 1 time 1091s 0 (0.00%) aligned concordantly >1 times 1091s ---- 1091s 72 pairs aligned concordantly 0 times; of these: 1091s 0 (0.00%) aligned discordantly 1 time 1091s ---- 1091s 72 pairs aligned 0 times concordantly or discordantly; of these: 1091s 144 mates make up the pairs; of these: 1091s 144 (100.00%) aligned 0 times 1091s 0 (0.00%) aligned exactly 1 time 1091s 0 (0.00%) aligned >1 times 1091s 0.00% overall alignment rate 1091s Read 50 alignments... 1091s Read 100 alignments... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s /usr/bin/bowtie2 --cp-min 5 --cp-ival 1 --mm --ma 8.97985814245788 -k 2 --np 5 --norc -R 3 --rfg 39.0503761229487 --score-min L,6.04579285806622,9.0245041461116 -q -p 2 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s --- Summary --- 1091s Read 1 reference strings 1091s Checked 0 alignments, 0 edits 1091s --------------- 1091s PASSED 1091s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1091s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1091s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #2 of read '11' because it was < 2 characters long 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1091s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1091s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1091s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #2 of read '57' because it was < 2 characters long 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1091s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1091s 72 reads; of these: 1091s 72 (100.00%) were paired; of these: 1091s 72 (100.00%) aligned concordantly 0 times 1091s 0 (0.00%) aligned concordantly exactly 1 time 1091s 0 (0.00%) aligned concordantly >1 times 1091s ---- 1091s 72 pairs aligned concordantly 0 times; of these: 1091s 0 (0.00%) aligned discordantly 1 time 1091s ---- 1091s 72 pairs aligned 0 times concordantly or discordantly; of these: 1091s 144 mates make up the pairs; of these: 1091s 144 (100.00%) aligned 0 times 1091s 0 (0.00%) aligned exactly 1 time 1091s 0 (0.00%) aligned >1 times 1091s 0.00% overall alignment rate 1091s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1091s Flattened IUPAC characters 1091s Mutating sequence Sim.pm.1 1091s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1091s Finished SNPs 1091s Finished ref gaps 1091s Finished read gaps 1091s Mutating sequence Sim.pm.2 1091s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1091s Finished SNPs 1091s Finished ref gaps 1091s Finished read gaps 1091s Mutated reference genome to subject genome 1091s SNPs introduced: 11 1091s Reference gaps introduced: 0 1091s Read gaps introduced: 0 1091s Rearrangements introduced: 0 1091s Created read sampler 1091s Sampling 76 reads 1091s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1091s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1091s parsing sequence Sim.pm.1... 1091s parsing sequence Sim.pm.2... 1091s Parsed 7 reference bases 1091s *** Run 58 of 100 1091s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 9 --np 5 --n-ceil 0.853455090915637,0.777391060757563 -k 3 --score-min L,6.44578475313806,5.58499064702737 --trim5 2 --trim3 3 --local -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw 1091s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1091s Warning: skipping read '1' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1091s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1091s Warning: skipping read '23' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '25' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '31' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1091s Warning: skipping mate #2 of read '42' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '48' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1091s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1091s Warning: skipping read '63' because it was < 2 characters long 1091s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 1091s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1091s 76 reads; of these: 1091s 68 (89.47%) were paired; of these: 1091s 68 (100.00%) aligned concordantly 0 times 1091s 0 (0.00%) aligned concordantly exactly 1 time 1091s 0 (0.00%) aligned concordantly >1 times 1091s ---- 1091s 68 pairs aligned concordantly 0 times; of these: 1091s 0 (0.00%) aligned discordantly 1 time 1091s ---- 1091s 68 pairs aligned 0 times concordantly or discordantly; of these: 1091s 136 mates make up the pairs; of these: 1091s 136 (100.00%) aligned 0 times 1091s 0 (0.00%) aligned exactly 1 time 1091s 0 (0.00%) aligned >1 times 1091s 8 (10.53%) were unpaired; of these: 1091s 8 (100.00%) aligned 0 times 1091s 0 (0.00%) aligned exactly 1 time 1091s 0 (0.00%) aligned >1 times 1091s 0.00% overall alignment rate 1091s Read 50 alignments... 1091s Read 100 alignments... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s Processing line... 1091s --- Summary --- 1091s Read 1 reference strings 1091s Checked 0 alignments, 0 edits 1091s --------------- 1091s PASSED 1091s Flattened IUPAC characters 1091s Mutating sequence Sim.pm.1 1091s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1091s Finished SNPs 1091s Finished ref gaps 1091s Finished read gaps 1091s Mutating sequence Sim.pm.2 1091s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1091s Finished SNPs 1091s Finished ref gaps 1091s Finished read gaps 1091s Mutated reference genome to subject genome 1091s SNPs introduced: 2 1091s Reference gaps introduced: 0 1091s Read gaps introduced: 0 1091s Rearrangements introduced: 0 1091s Created read sampler 1091s Sampling 122 reads 1091s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1091s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1091s parsing sequence Sim.pm.1... 1091s *** Run 59 of 100 1091s /usr/bin/bowtie2 -i L,0.00520384658236381 --n-ceil 1.22968764092003,0.569965257051888 --score-min L,4.07397836041086,1.09293835326087 --nofw --norc -D 4 -a --rdg 24.9147500050039,14.8921105865526 --local --cp-min 3 --cp-ival 1 -q -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq 1091s parsing sequence Sim.pm.2... 1091s Parsed 7 reference bases 1092s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '7' because it was < 2 characters long 1092s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '11' because it was < 2 characters long 1092s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '25' because it was < 2 characters long 1092s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '35' because it was < 2 characters long 1092s Warning: skipping read '67' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '67' because it was < 2 characters long 1092s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '77' because it was < 2 characters long 1092s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '92' because it was < 2 characters long 1092s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '102' because it was < 2 characters long 1092s 122 reads; of these: 1092s 122 (100.00%) were unpaired; of these: 1092s 122 (100.00%) aligned 0 times 1092s 0 (0.00%) aligned exactly 1 time 1092s 0 (0.00%) aligned >1 times 1092s 0.00% overall alignment rate 1092s Read 50 alignments... 1092s Read 100 alignments... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s --- Summary --- 1092s Read 1 reference strings 1092s Checked 0 alignments, 0 edits 1092s --------------- 1092s PASSED 1092s ALSO checking that bowtie2 and bowtie2-align match up 1092s /usr/bin/bowtie2 -i L,0.00520384658236381 --n-ceil 1.22968764092003,0.569965257051888 --score-min L,4.07397836041086,1.09293835326087 --nofw --norc -D 4 -a --rdg 24.9147500050039,14.8921105865526 --local --cp-min 3 --cp-ival 1 -q -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1092s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '7' because it was < 2 characters long 1092s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '11' because it was < 2 characters long 1092s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '25' because it was < 2 characters long 1092s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '35' because it was < 2 characters long 1092s Warning: skipping read '67' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '67' because it was < 2 characters long 1092s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '77' because it was < 2 characters long 1092s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '92' because it was < 2 characters long 1092s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read '102' because it was < 2 characters long 1092s 122 reads; of these: 1092s 122 (100.00%) were unpaired; of these: 1092s 122 (100.00%) aligned 0 times 1092s 0 (0.00%) aligned exactly 1 time 1092s 0 (0.00%) aligned >1 times 1092s 0.00% overall alignment rate 1092s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1092s Flattened IUPAC characters 1092s Mutating sequence Sim.pm.1 1092s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1092s Finished SNPs 1092s Finished ref gaps 1092s Finished read gaps 1092s Mutating sequence Sim.pm.2 1092s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1092s Finished SNPs 1092s Finished ref gaps 1092s Finished read gaps 1092s Mutated reference genome to subject genome 1092s SNPs introduced: 5 1092s Reference gaps introduced: 0 1092s Read gaps introduced: 0 1092s Rearrangements introduced: 1 1092s Created read sampler 1092s Sampling 48 reads 1092s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1092s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1092s parsing sequence Sim.pm.1... 1092s parsing sequence Sim.pm.2... 1092s Parsed 7 reference bases 1092s *** Run 60 of 100 1092s /usr/bin/bowtie2 --nofw --np 3 -R 3 -N 0 -L12 --score-min L,2.21229405749822,2.68346087778647 --cp-min 3 --cp-ival 1 --local --rdg 37.560612460902,2.25323212729987 -M 3 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1092s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1092s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 1092s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1092s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 1092s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1092s 48 reads; of these: 1092s 48 (100.00%) were unpaired; of these: 1092s 48 (100.00%) aligned 0 times 1092s 0 (0.00%) aligned exactly 1 time 1092s 0 (0.00%) aligned >1 times 1092s 0.00% overall alignment rate 1092s Read 50 alignments... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s --- Summary --- 1092s Read 1 reference strings 1092s Checked 0 alignments, 0 edits 1092s --------------- 1092s PASSED 1092s Flattened IUPAC characters 1092s Mutating sequence Sim.pm.2 1092s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1092s Finished SNPs 1092s Finished ref gaps 1092s Finished read gaps 1092s Mutating sequence Sim.pm.1 1092s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1092s Finished SNPs 1092s Finished ref gaps 1092s Finished read gaps 1092s Mutated reference genome to subject genome 1092s SNPs introduced: 2 1092s Reference gaps introduced: 0 1092s Read gaps introduced: 1 1092s Rearrangements introduced: 0 1092s Created read sampler 1092s Sampling 48 reads 1092s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1092s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1092s parsing sequence Sim.pm.1... 1092s parsing sequence Sim.pm.2... 1092s Parsed 7 reference bases 1092s *** Run 61 of 100 1092s /usr/bin/bowtie2 --trim5 6 --rfg 26.0741149877663,17.2202814313229 --gbar 4 --score-min L,5.81317483965301,2.63488072294968 --rdg 40.7884337324728 --mp 6.33191692513085,2.50574237433639 --trim3 4 --ma 29.0006011245079 -k 3 --cp-min 2 --mm --cp-ival 1 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1092s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1092s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '2' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1092s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '3' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1092s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '4' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1092s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '5' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1092s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '6' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1092s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '7' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1092s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '8' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1092s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '9' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1092s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '12' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1092s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '13' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1092s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '20' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1092s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '29' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1092s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '31' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1092s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '32' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1092s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '35' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1092s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '37' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1092s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '39' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1092s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '40' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1092s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1092s Warning: skipping read '41' because it was < 2 characters long 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1092s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1092s 48 reads; of these: 1092s 48 (100.00%) were unpaired; of these: 1092s 48 (100.00%) aligned 0 times 1092s 0 (0.00%) aligned exactly 1 time 1092s 0 (0.00%) aligned >1 times 1092s 0.00% overall alignment rate 1092s Read 50 alignments... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s Processing line... 1092s --- Summary --- 1092s Read 1 reference strings 1092s Checked 0 alignments, 0 edits 1092s --------------- 1092s PASSED 1092s ALSO checking that bowtie2 and bowtie2-align match up 1092s /usr/bin/bowtie2 --trim5 6 --rfg 26.0741149877663,17.2202814313229 --gbar 4 --score-min L,5.81317483965301,2.63488072294968 --rdg 40.7884337324728 --mp 6.33191692513085,2.50574237433639 --trim3 4 --ma 29.0006011245079 -k 3 --cp-min 2 --mm --cp-ival 1 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1092s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1093s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '2' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1093s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '3' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1093s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '4' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1093s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '5' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1093s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '6' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1093s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '7' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1093s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '8' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1093s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '9' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1093s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '12' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1093s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '13' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1093s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '20' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1093s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '29' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1093s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '31' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1093s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '32' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1093s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '35' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1093s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '37' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1093s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '39' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1093s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '40' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1093s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '41' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1093s 48 reads; of these: 1093s 48 (100.00%) were unpaired; of these: 1093s 48 (100.00%) aligned 0 times 1093s 0 (0.00%) aligned exactly 1 time 1093s 0 (0.00%) aligned >1 times 1093s 0.00% overall alignment rate 1093s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1093s /usr/bin/bowtie2 --trim5 6 --rfg 26.0741149877663,17.2202814313229 --gbar 4 --score-min L,5.81317483965301,2.63488072294968 --rdg 40.7884337324728 --mp 6.33191692513085,2.50574237433639 --trim3 4 --ma 29.0006011245079 -k 3 --cp-min 2 --mm --cp-ival 1 -r -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1093s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1093s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1093s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '2' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1093s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '3' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1093s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '4' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1093s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '5' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1093s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '6' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1093s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '7' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1093s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '8' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1093s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '9' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1093s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '12' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1093s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '13' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1093s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '20' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1093s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '29' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1093s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '31' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1093s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '32' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1093s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '35' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1093s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '37' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1093s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '39' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1093s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '40' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1093s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '41' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1093s 48 reads; of these: 1093s 48 (100.00%) were unpaired; of these: 1093s 48 (100.00%) aligned 0 times 1093s 0 (0.00%) aligned exactly 1 time 1093s 0 (0.00%) aligned >1 times 1093s 0.00% overall alignment rate 1093s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1093s *** Run 62 of 100 1093s /usr/bin/bowtie2 --rfg 20.1556414348211,16.4049488806262 --rdg 40.0560431181284 --trim5 7 --score-min L,5.01087516728993,4.94359944071898 --ma 23.7571496476222 --cp-min 3 --cp-ival 4 --mm -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1093s Flattened IUPAC characters 1093s Mutating sequence Sim.pm.1 1093s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1093s Finished SNPs 1093s Finished ref gaps 1093s Finished read gaps 1093s Mutating sequence Sim.pm.2 1093s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1093s Finished SNPs 1093s Finished ref gaps 1093s Finished read gaps 1093s Mutated reference genome to subject genome 1093s SNPs introduced: 7 1093s Reference gaps introduced: 1 1093s Read gaps introduced: 0 1093s Rearrangements introduced: 0 1093s Created read sampler 1093s Sampling 47 reads 1093s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1093s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1093s parsing sequence Sim.pm.1... 1093s parsing sequence Sim.pm.2... 1093s Parsed 7 reference bases 1093s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1093s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '1' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1093s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '6' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1093s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '8' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1093s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '15' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1093s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '19' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1093s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '23' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1093s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '27' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1093s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '28' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1093s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '29' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1093s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '30' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1093s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '31' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1093s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '33' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1093s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '44' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1093s 47 reads; of these: 1093s 47 (100.00%) were unpaired; of these: 1093s 45 (95.74%) aligned 0 times 1093s 2 (4.26%) aligned exactly 1 time 1093s 0 (0.00%) aligned >1 times 1093s 4.26% overall alignment rate 1093s Read 50 alignments... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s /usr/bin/bowtie2 --rfg 20.1556414348211,16.4049488806262 --rdg 40.0560431181284 --trim5 7 --score-min L,5.01087516728993,4.94359944071898 --ma 23.7571496476222 --cp-min 3 --cp-ival 4 --mm -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s GG 1093s GG 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s GAGGTA 1093s GAGGTA 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s Processing line... 1093s --- Summary --- 1093s Read 1 reference strings 1093s Checked 2 alignments, 0 edits 1093s --------------- 1093s PASSED 1093s ALSO checking that bowtie2 and bowtie2-align match up 1093s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1093s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '1' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1093s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '6' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1093s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '8' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1093s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '15' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1093s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '19' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1093s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '23' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1093s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '27' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1093s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '28' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1093s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '29' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1093s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '30' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1093s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '31' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1093s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '33' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1093s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '44' because it was < 2 characters long 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1093s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1093s 47 reads; of these: 1093s 47 (100.00%) were unpaired; of these: 1093s 45 (95.74%) aligned 0 times 1093s 2 (4.26%) aligned exactly 1 time 1093s 0 (0.00%) aligned >1 times 1093s 4.26% overall alignment rate 1093s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1093s Flattened IUPAC characters 1093s Mutating sequence Sim.pm.1 1093s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1093s Finished SNPs 1093s Finished ref gaps 1093s Finished read gaps 1093s Mutating sequence Sim.pm.2 1093s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1093s Finished SNPs 1093s Finished ref gaps 1093s Finished read gaps 1093s Mutated reference genome to subject genome 1093s SNPs introduced: 10 1093s Reference gaps introduced: 1 1093s Read gaps introduced: 0 1093s Rearrangements introduced: 1 1093s Created read sampler 1093s Sampling 120 reads 1093s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1093s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1093s parsing sequence Sim.pm.1... 1093s *** Run 63 of 100 1093s /usr/bin/bowtie2 --cp-min 3 --mm --cp-ival 1 --local --mp 8.92755553398385,7.14942751857515 -k 2 --norc --np 3 -R 3 -i L,0.250301894860184 --trim5 2 --score-min L,1.81880274349741,3.00958708897927 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1093s parsing sequence Sim.pm.2... 1093s Parsed 7 reference bases 1093s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '13' because it was < 2 characters long 1093s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '14' because it was < 2 characters long 1093s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '17' because it was < 2 characters long 1093s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '21' because it was < 2 characters long 1093s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1093s Warning: skipping read '29' because it was < 2 characters long 1093s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '35' because it was < 2 characters long 1093s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '38' because it was < 2 characters long 1093s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '54' because it was < 2 characters long 1093s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1093s Warning: skipping read '59' because it was < 2 characters long 1094s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '83' because it was < 2 characters long 1094s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '88' because it was < 2 characters long 1094s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '107' because it was < 2 characters long 1094s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '115' because it was < 2 characters long 1094s 120 reads; of these: 1094s 120 (100.00%) were unpaired; of these: 1094s 120 (100.00%) aligned 0 times 1094s 0 (0.00%) aligned exactly 1 time 1094s 0 (0.00%) aligned >1 times 1094s 0.00% overall alignment rate 1094s Read 50 alignments... 1094s Read 100 alignments... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s --- Summary --- 1094s Read 1 reference strings 1094s Checked 0 alignments, 0 edits 1094s --------------- 1094s PASSED 1094s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1094s /usr/bin/bowtie2 --cp-min 3 --mm --cp-ival 1 --local --mp 8.92755553398385,7.14942751857515 -k 2 --norc --np 3 -R 3 -i L,0.250301894860184 --trim5 2 --score-min L,1.81880274349741,3.00958708897927 -f -p 2 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1094s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '13' because it was < 2 characters long 1094s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '14' because it was < 2 characters long 1094s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '17' because it was < 2 characters long 1094s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '21' because it was < 2 characters long 1094s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '35' because it was < 2 characters long 1094s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '38' because it was < 2 characters long 1094s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '54' because it was < 2 characters long 1094s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '59' because it was < 2 characters long 1094s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '29' because it was < 2 characters long 1094s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '83' because it was < 2 characters long 1094s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '88' because it was < 2 characters long 1094s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '115' because it was < 2 characters long 1094s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '107' because it was < 2 characters long 1094s 120 reads; of these: 1094s 120 (100.00%) were unpaired; of these: 1094s 120 (100.00%) aligned 0 times 1094s 0 (0.00%) aligned exactly 1 time 1094s 0 (0.00%) aligned >1 times 1094s 0.00% overall alignment rate 1094s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1094s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1094s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1094s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1094s /usr/bin/bowtie2 --cp-min 3 --mm --cp-ival 1 --local --mp 8.92755553398385,7.14942751857515 -k 2 --norc --np 3 -R 3 -i L,0.250301894860184 --trim5 2 --score-min L,1.81880274349741,3.00958708897927 -f -p 4 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1094s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '13' because it was < 2 characters long 1094s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '14' because it was < 2 characters long 1094s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '17' because it was < 2 characters long 1094s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '21' because it was < 2 characters long 1094s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '29' because it was < 2 characters long 1094s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '35' because it was < 2 characters long 1094s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '38' because it was < 2 characters long 1094s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '54' because it was < 2 characters long 1094s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '59' because it was < 2 characters long 1094s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '107' because it was < 2 characters long 1094s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '115' because it was < 2 characters long 1094s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1094s Warning: skipping read '83' because it was < 2 characters long 1094s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 1094s Warning: skipping read '88' because it was < 2 characters long 1094s 120 reads; of these: 1094s 120 (100.00%) were unpaired; of these: 1094s 120 (100.00%) aligned 0 times 1094s 0 (0.00%) aligned exactly 1 time 1094s 0 (0.00%) aligned >1 times 1094s 0.00% overall alignment rate 1094s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1094s Flattened IUPAC characters 1094s Mutating sequence Sim.pm.1 1094s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1094s Finished SNPs 1094s Finished ref gaps 1094s Finished read gaps 1094s Mutating sequence Sim.pm.2 1094s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1094s Finished SNPs 1094s Finished ref gaps 1094s Finished read gaps 1094s Mutated reference genome to subject genome 1094s SNPs introduced: 10 1094s Reference gaps introduced: 0 1094s Read gaps introduced: 0 1094s Rearrangements introduced: 1 1094s Created read sampler 1094s Sampling 22 reads 1094s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1094s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1094s parsing sequence Sim.pm.1... 1094s parsing sequence Sim.pm.2... 1094s Parsed 7 reference bases 1094s *** Run 64 of 100 1094s /usr/bin/bowtie2 --local --rdg 33.4348404123268 --mp 5.55192337553645,3.95753490337658 -a --cp-ival 1 --cp-min 2 --score-min L,6.56835601446697,8.46760588406888 --rfg 47.218737936389,17.0206104557737 -R 1 -D 13 --norc --np 7 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1094s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 1094s Warning: skipping mate #2 of read '15' because it was < 2 characters long 1094s 22 reads; of these: 1094s 22 (100.00%) were paired; of these: 1094s 22 (100.00%) aligned concordantly 0 times 1094s 0 (0.00%) aligned concordantly exactly 1 time 1094s 0 (0.00%) aligned concordantly >1 times 1094s ---- 1094s 22 pairs aligned concordantly 0 times; of these: 1094s 0 (0.00%) aligned discordantly 1 time 1094s ---- 1094s 22 pairs aligned 0 times concordantly or discordantly; of these: 1094s 44 mates make up the pairs; of these: 1094s 44 (100.00%) aligned 0 times 1094s 0 (0.00%) aligned exactly 1 time 1094s 0 (0.00%) aligned >1 times 1094s 0.00% overall alignment rate 1094s /usr/bin/bowtie2 --local --rdg 33.4348404123268 --mp 5.55192337553645,3.95753490337658 -a --cp-ival 1 --cp-min 2 --score-min L,6.56835601446697,8.46760588406888 --rfg 47.218737936389,17.0206104557737 -R 1 -D 13 --norc --np 7 -f -p 2 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s Processing line... 1094s --- Summary --- 1094s Read 1 reference strings 1094s Checked 0 alignments, 0 edits 1094s --------------- 1094s PASSED 1094s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1095s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 1095s Warning: skipping mate #2 of read '15' because it was < 2 characters long 1095s 22 reads; of these: 1095s 22 (100.00%) were paired; of these: 1095s 22 (100.00%) aligned concordantly 0 times 1095s 0 (0.00%) aligned concordantly exactly 1 time 1095s 0 (0.00%) aligned concordantly >1 times 1095s ---- 1095s 22 pairs aligned concordantly 0 times; of these: 1095s 0 (0.00%) aligned discordantly 1 time 1095s ---- 1095s 22 pairs aligned 0 times concordantly or discordantly; of these: 1095s 44 mates make up the pairs; of these: 1095s 44 (100.00%) aligned 0 times 1095s 0 (0.00%) aligned exactly 1 time 1095s 0 (0.00%) aligned >1 times 1095s 0.00% overall alignment rate 1095s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1095s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1095s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1095s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1095s /usr/bin/bowtie2 --local --rdg 33.4348404123268 --mp 5.55192337553645,3.95753490337658 -a --cp-ival 1 --cp-min 2 --score-min L,6.56835601446697,8.46760588406888 --rfg 47.218737936389,17.0206104557737 -R 1 -D 13 --norc --np 7 -f -p 2 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1095s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 1095s Warning: skipping mate #2 of read '15' because it was < 2 characters long 1095s 22 reads; of these: 1095s 22 (100.00%) were paired; of these: 1095s 22 (100.00%) aligned concordantly 0 times 1095s 0 (0.00%) aligned concordantly exactly 1 time 1095s 0 (0.00%) aligned concordantly >1 times 1095s ---- 1095s 22 pairs aligned concordantly 0 times; of these: 1095s 0 (0.00%) aligned discordantly 1 time 1095s ---- 1095s 22 pairs aligned 0 times concordantly or discordantly; of these: 1095s 44 mates make up the pairs; of these: 1095s 44 (100.00%) aligned 0 times 1095s 0 (0.00%) aligned exactly 1 time 1095s 0 (0.00%) aligned >1 times 1095s 0.00% overall alignment rate 1095s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1095s Flattened IUPAC characters 1095s Mutating sequence Sim.pm.2 1095s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1095s Finished SNPs 1095s Finished ref gaps 1095s Finished read gaps 1095s Mutating sequence Sim.pm.1 1095s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1095s Finished SNPs 1095s Finished ref gaps 1095s Finished read gaps 1095s Mutated reference genome to subject genome 1095s SNPs introduced: 6 1095s Reference gaps introduced: 0 1095s Read gaps introduced: 0 1095s Rearrangements introduced: 1 1095s Created read sampler 1095s Sampling 74 reads 1095s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1095s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1095s parsing sequence Sim.pm.1... 1095s parsing sequence Sim.pm.2... 1095s Parsed 7 reference bases 1095s *** Run 65 of 100 1095s /usr/bin/bowtie2 --cp-min 9 --mm --cp-ival 1 --local --rdg 47.5349919244062 -M 5 --norc --nofw -D 19 --rfg 40.587940489396 --score-min L,5.96921968524515,9.70442793931644 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1095s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1095s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 1095s Warning: skipping mate #1 of read '25' because it was < 2 characters long 1095s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 1095s Read 50 alignments... 1095s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1095s Read 100 alignments... 1095s 74 reads; of these: 1095s 74 (100.00%) were paired; of these: 1095s 74 (100.00%) aligned concordantly 0 times 1095s 0 (0.00%) aligned concordantly exactly 1 time 1095s 0 (0.00%) aligned concordantly >1 times 1095s ---- 1095s 74 pairs aligned concordantly 0 times; of these: 1095s 0 (0.00%) aligned discordantly 1 time 1095s ---- 1095s 74 pairs aligned 0 times concordantly or discordantly; of these: 1095s 148 mates make up the pairs; of these: 1095s 148 (100.00%) aligned 0 times 1095s 0 (0.00%) aligned exactly 1 time 1095s 0 (0.00%) aligned >1 times 1095s 0.00% overall alignment rate 1095s Read 150 alignments... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s Processing line... 1095s --- Summary --- 1095s Read 1 reference strings 1095s Checked 0 alignments, 0 edits 1095s --------------- 1095s PASSED 1095s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1095s /usr/bin/bowtie2 --cp-min 9 --mm --cp-ival 1 --local --rdg 47.5349919244062 -M 5 --norc --nofw -D 19 --rfg 40.587940489396 --score-min L,5.96921968524515,9.70442793931644 -q -p 4 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1096s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1096s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 1096s Warning: skipping mate #1 of read '25' because it was < 2 characters long 1096s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 1096s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1096s 74 reads; of these: 1096s 74 (100.00%) were paired; of these: 1096s 74 (100.00%) aligned concordantly 0 times 1096s 0 (0.00%) aligned concordantly exactly 1 time 1096s 0 (0.00%) aligned concordantly >1 times 1096s ---- 1096s 74 pairs aligned concordantly 0 times; of these: 1096s 0 (0.00%) aligned discordantly 1 time 1096s ---- 1096s 74 pairs aligned 0 times concordantly or discordantly; of these: 1096s 148 mates make up the pairs; of these: 1096s 148 (100.00%) aligned 0 times 1096s 0 (0.00%) aligned exactly 1 time 1096s 0 (0.00%) aligned >1 times 1096s 0.00% overall alignment rate 1096s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1096s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1096s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1096s /usr/bin/bowtie2 --cp-min 9 --mm --cp-ival 1 --local --rdg 47.5349919244062 -M 5 --norc --nofw -D 19 --rfg 40.587940489396 --score-min L,5.96921968524515,9.70442793931644 -q -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1096s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1096s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1096s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 1096s Warning: skipping mate #1 of read '25' because it was < 2 characters long 1096s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 1096s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1096s 74 reads; of these: 1096s 74 (100.00%) were paired; of these: 1096s 74 (100.00%) aligned concordantly 0 times 1096s 0 (0.00%) aligned concordantly exactly 1 time 1096s 0 (0.00%) aligned concordantly >1 times 1096s ---- 1096s 74 pairs aligned concordantly 0 times; of these: 1096s 0 (0.00%) aligned discordantly 1 time 1096s ---- 1096s 74 pairs aligned 0 times concordantly or discordantly; of these: 1096s 148 mates make up the pairs; of these: 1096s 148 (100.00%) aligned 0 times 1096s 0 (0.00%) aligned exactly 1 time 1096s 0 (0.00%) aligned >1 times 1096s 0.00% overall alignment rate 1096s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1096s Flattened IUPAC characters 1096s Mutating sequence Sim.pm.2 1096s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1096s Finished SNPs 1096s Finished ref gaps 1096s Finished read gaps 1096s Mutating sequence Sim.pm.1 1096s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1096s Finished SNPs 1096s Finished ref gaps 1096s Finished read gaps 1096s Mutated reference genome to subject genome 1096s SNPs introduced: 6 1096s Reference gaps introduced: 0 1096s Read gaps introduced: 2 1096s Rearrangements introduced: 0 1096s Created read sampler 1096s Sampling 78 reads 1096s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1096s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1096s parsing sequence Sim.pm.1... 1096s parsing sequence Sim.pm.2... 1096s Parsed 7 reference bases 1096s *** Run 66 of 100 1096s /usr/bin/bowtie2 --trim3 8 --mp 7.36068627594893,6.3941302166791 -k 7 --ma 20.232248730837 --cp-min 2 --cp-ival 1 --trim5 2 --gbar 5 --score-min L,2.1387820648013,2.29075733279547 -R 2 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1096s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1096s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '0' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1096s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '2' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1096s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '5' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1096s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '6' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1096s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '9' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1096s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '10' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1096s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '14' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1096s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '15' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1096s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '21' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1096s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '22' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1096s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '23' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1096s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '25' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1096s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '29' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1096s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '34' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1096s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '35' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1096s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '39' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1096s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '48' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1096s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '49' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1096s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '50' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1096s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '61' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1096s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '63' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1096s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '65' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1096s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '67' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1096s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '68' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1096s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '69' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1096s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 1096s Warning: skipping read '76' because it was < 2 characters long 1096s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1096s 78 reads; of these: 1096s 78 (100.00%) were unpaired; of these: 1096s 75 (96.15%) aligned 0 times 1096s 2 (2.56%) aligned exactly 1 time 1096s 1 (1.28%) aligned >1 times 1096s 3.85% overall alignment rate 1096s Read 50 alignments... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s GA 1096s GA 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s GA 1096s GA 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s TA 1096s TA 1096s Processing line... 1096s TA 1096s TA 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s Processing line... 1096s --- Summary --- 1096s Read 1 reference strings 1096s Checked 4 alignments, 0 edits 1096s --------------- 1096s PASSED 1096s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1096s /usr/bin/bowtie2 --trim3 8 --mp 7.36068627594893,6.3941302166791 -k 7 --ma 20.232248730837 --cp-min 2 --cp-ival 1 --trim5 2 --gbar 5 --score-min L,2.1387820648013,2.29075733279547 -R 2 -r -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1097s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1097s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '0' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1097s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '2' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1097s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '21' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1097s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '22' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1097s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '23' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1097s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '25' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1097s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '29' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1097s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '34' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1097s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '35' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1097s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '39' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1097s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '5' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1097s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '6' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1097s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '9' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1097s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '10' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1097s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '14' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1097s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '15' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1097s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '48' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1097s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '49' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1097s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '50' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1097s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '61' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1097s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '63' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1097s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '65' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1097s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '67' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1097s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '68' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1097s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '69' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1097s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 1097s Warning: skipping read '76' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1097s 78 reads; of these: 1097s 78 (100.00%) were unpaired; of these: 1097s 75 (96.15%) aligned 0 times 1097s 2 (2.56%) aligned exactly 1 time 1097s 1 (1.28%) aligned >1 times 1097s 3.85% overall alignment rate 1097s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1097s Flattened IUPAC characters 1097s Mutating sequence Sim.pm.2 1097s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1097s Finished SNPs 1097s Finished ref gaps 1097s Finished read gaps 1097s Mutating sequence Sim.pm.1 1097s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1097s Finished SNPs 1097s Finished ref gaps 1097s Finished read gaps 1097s Mutated reference genome to subject genome 1097s SNPs introduced: 1 1097s Reference gaps introduced: 0 1097s Read gaps introduced: 1 1097s Rearrangements introduced: 0 1097s Created read sampler 1097s Sampling 91 reads 1097s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1097s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1097s parsing sequence Sim.pm.1... 1097s parsing sequence Sim.pm.2... 1097s Parsed 7 reference bases 1097s *** Run 67 of 100 1097s /usr/bin/bowtie2 --np 4 --nofw --cp-min 2 -D 46 --cp-ival 1 -i L,0.0670299032691595 --mp 6.8413265657205,2.51927254355427 --score-min L,4.30539207111966,6.18254901585945 -M 3 -q -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq 1097s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1097s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '23' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1097s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '51' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1097s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '56' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1097s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '76' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1097s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '77' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1097s Warning: skipping read '84' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '84' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1097s 91 reads; of these: 1097s 91 (100.00%) were unpaired; of these: 1097s 90 (98.90%) aligned 0 times 1097s 1 (1.10%) aligned exactly 1 time 1097s 0 (0.00%) aligned >1 times 1097s 1.10% overall alignment rate 1097s Read 50 alignments... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s GG 1097s GG 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s Processing line... 1097s --- Summary --- 1097s Read 1 reference strings 1097s Checked 1 alignments, 0 edits 1097s --------------- 1097s PASSED 1097s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1097s /usr/bin/bowtie2 --np 4 --nofw --cp-min 2 -D 46 --cp-ival 1 -i L,0.0670299032691595 --mp 6.8413265657205,2.51927254355427 --score-min L,4.30539207111966,6.18254901585945 -M 3 -q -p 2 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1097s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1097s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '23' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1097s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '76' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1097s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '77' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1097s Warning: skipping read '84' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '84' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1097s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '51' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1097s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 1097s Warning: skipping read '56' because it was < 2 characters long 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1097s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1097s 91 reads; of these: 1097s 91 (100.00%) were unpaired; of these: 1097s 90 (98.90%) aligned 0 times 1097s 1 (1.10%) aligned exactly 1 time 1097s 0 (0.00%) aligned >1 times 1097s 1.10% overall alignment rate 1097s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1097s Flattened IUPAC characters 1097s Mutating sequence Sim.pm.1 1097s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1097s Finished SNPs 1097s Finished ref gaps 1097s Finished read gaps 1097s Mutating sequence Sim.pm.2 1097s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1097s Finished SNPs 1097s Finished ref gaps 1097s Finished read gaps 1097s Mutated reference genome to subject genome 1097s SNPs introduced: 10 1097s Reference gaps introduced: 0 1097s Read gaps introduced: 1 1097s Rearrangements introduced: 0 1097s Created read sampler 1097s Sampling 160 reads 1097s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1097s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1097s parsing sequence Sim.pm.1... 1097s parsing sequence Sim.pm.2... 1097s Parsed 7 reference bases 1097s *** Run 68 of 100 1097s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --np 3 -M 8 --score-min L,5.57965333586118,5.53271706927612 --rdg 44.8714311574919 --local --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1097s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1098s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 1098s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1098s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 1098s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1098s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 1098s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 1098s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 1098s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 1098s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (1) <= # seed mismatches (0) 1098s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1098s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (0) 1098s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 1098s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (1) <= # seed mismatches (0) 1098s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 1098s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (1) <= # seed mismatches (0) 1098s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 1098s Warning: skipping read 'R_1_1_1_156_156_1/1' because length (1) <= # seed mismatches (0) 1098s Warning: skipping read 'R_1_1_1_156_156_1/1' because it was < 2 characters long 1098s 160 reads; of these: 1098s 160 (100.00%) were unpaired; of these: 1098s 160 (100.00%) aligned 0 times 1098s 0 (0.00%) aligned exactly 1 time 1098s 0 (0.00%) aligned >1 times 1098s 0.00% overall alignment rate 1098s Read 50 alignments... 1098s Read 100 alignments... 1098s Read 150 alignments... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 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1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s --- Summary --- 1098s Read 1 reference strings 1098s Checked 0 alignments, 0 edits 1098s --------------- 1098s PASSED 1098s Flattened IUPAC characters 1098s Mutating sequence Sim.pm.1 1098s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1098s Finished SNPs 1098s Finished ref gaps 1098s Finished read gaps 1098s Mutating sequence Sim.pm.2 1098s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1098s Finished SNPs 1098s Finished ref gaps 1098s Finished read gaps 1098s Mutated reference genome to subject genome 1098s SNPs introduced: 0 1098s Reference gaps introduced: 0 1098s Read gaps introduced: 0 1098s Rearrangements introduced: 1 1098s Created read sampler 1098s Sampling 19 reads 1098s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1098s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1098s parsing sequence Sim.pm.1... 1098s parsing sequence Sim.pm.2... 1098s Parsed 7 reference bases 1098s *** Run 69 of 100 1098s /usr/bin/bowtie2 --rfg 23.2664355955306 --trim3 6 --score-min L,1.13861622790917,9.7689425453358 --norc --cp-min 2 --cp-ival 1 -R 2 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1098s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 1098s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1098s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 1098s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1098s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1098s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 1098s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1098s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1098s Warning: skipping read '16' because it was < 2 characters long 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1098s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1098s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1098s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1098s 19 reads; of these: 1098s 14 (73.68%) were paired; of these: 1098s 14 (100.00%) aligned concordantly 0 times 1098s 0 (0.00%) aligned concordantly exactly 1 time 1098s 0 (0.00%) aligned concordantly >1 times 1098s ---- 1098s 14 pairs aligned concordantly 0 times; of these: 1098s 0 (0.00%) aligned discordantly 1 time 1098s ---- 1098s 14 pairs aligned 0 times concordantly or discordantly; of these: 1098s 28 mates make up the pairs; of these: 1098s 27 (96.43%) aligned 0 times 1098s 1 (3.57%) aligned exactly 1 time 1098s 0 (0.00%) aligned >1 times 1098s 5 (26.32%) were unpaired; of these: 1098s 5 (100.00%) aligned 0 times 1098s 0 (0.00%) aligned exactly 1 time 1098s 0 (0.00%) aligned >1 times 1098s 3.03% overall alignment rate 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s TA 1098s TA 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s Processing line... 1098s --- Summary --- 1098s Read 1 reference strings 1098s Checked 1 alignments, 0 edits 1098s --------------- 1098s PASSED 1098s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1098s /usr/bin/bowtie2 --rfg 23.2664355955306 --trim3 6 --score-min L,1.13861622790917,9.7689425453358 --norc --cp-min 2 --cp-ival 1 -R 2 -f -p 2 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1098s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1098s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1098s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1098s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 1098s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1098s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 1098s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1098s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1098s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 1098s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1098s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1098s Warning: skipping read '16' because it was < 2 characters long 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1098s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1098s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1098s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1098s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1098s 19 reads; of these: 1098s 14 (73.68%) were paired; of these: 1098s 14 (100.00%) aligned concordantly 0 times 1098s 0 (0.00%) aligned concordantly exactly 1 time 1098s 0 (0.00%) aligned concordantly >1 times 1098s ---- 1098s 14 pairs aligned concordantly 0 times; of these: 1098s 0 (0.00%) aligned discordantly 1 time 1098s ---- 1098s 14 pairs aligned 0 times concordantly or discordantly; of these: 1098s 28 mates make up the pairs; of these: 1098s 27 (96.43%) aligned 0 times 1098s 1 (3.57%) aligned exactly 1 time 1098s 0 (0.00%) aligned >1 times 1098s 5 (26.32%) were unpaired; of these: 1098s 5 (100.00%) aligned 0 times 1098s 0 (0.00%) aligned exactly 1 time 1098s 0 (0.00%) aligned >1 times 1098s 3.03% overall alignment rate 1098s *** Run 70 of 100 1098s /usr/bin/bowtie2 --cp-min 8 --cp-ival 1 --local --trim3 5 --mp 3.57794076023855,2.27653545537289 -M 2 --np 8 -R 3 -i S,2.64146766230685,6.77974405571737 --trim5 4 --score-min L,4.71594753668436,9.70352306254183 -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw 1098s Flattened IUPAC characters 1098s Mutating sequence Sim.pm.2 1098s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1098s Finished SNPs 1098s Finished ref gaps 1098s Finished read gaps 1098s Mutating sequence Sim.pm.1 1098s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1098s Finished SNPs 1098s Finished ref gaps 1098s Finished read gaps 1098s Mutated reference genome to subject genome 1098s SNPs introduced: 2 1098s Reference gaps introduced: 0 1098s Read gaps introduced: 0 1098s Rearrangements introduced: 0 1098s Created read sampler 1098s Sampling 51 reads 1098s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1098s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1098s parsing sequence Sim.pm.1... 1098s parsing sequence Sim.pm.2... 1098s Parsed 7 reference bases 1099s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1099s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1099s Warning: skipping mate #2 of read '34' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1099s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 1099s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1099s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 1099s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1099s 51 reads; of these: 1099s 45 (88.24%) were paired; of these: 1099s 45 (100.00%) aligned concordantly 0 times 1099s 0 (0.00%) aligned concordantly exactly 1 time 1099s 0 (0.00%) aligned concordantly >1 times 1099s ---- 1099s 45 pairs aligned concordantly 0 times; of these: 1099s 0 (0.00%) aligned discordantly 1 time 1099s ---- 1099s 45 pairs aligned 0 times concordantly or discordantly; of these: 1099s 90 mates make up the pairs; of these: 1099s 90 (100.00%) aligned 0 times 1099s 0 (0.00%) aligned exactly 1 time 1099s 0 (0.00%) aligned >1 times 1099s 6 (11.76%) were unpaired; of these: 1099s 6 (100.00%) aligned 0 times 1099s 0 (0.00%) aligned exactly 1 time 1099s 0 (0.00%) aligned >1 times 1099s 0.00% overall alignment rate 1099s Read 50 alignments... 1099s Read 100 alignments... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s --- Summary --- 1099s Read 1 reference strings 1099s Checked 0 alignments, 0 edits 1099s --------------- 1099s PASSED 1099s Flattened IUPAC characters 1099s Mutating sequence Sim.pm.2 1099s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1099s Finished SNPs 1099s Finished ref gaps 1099s Finished read gaps 1099s Mutating sequence Sim.pm.1 1099s Introducing 5 SNPs, 0/2 ref/read gaps, and 1 rearrangements 1099s Finished SNPs 1099s Finished ref gaps 1099s Finished read gaps 1099s Mutated reference genome to subject genome 1099s SNPs introduced: 5 1099s Reference gaps introduced: 0 1099s Read gaps introduced: 2 1099s Rearrangements introduced: 1 1099s Created read sampler 1099s Sampling 52 reads 1099s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1099s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1099s parsing sequence Sim.pm.1... 1099s parsing sequence Sim.pm.2... 1099s Parsed 7 reference bases 1099s *** Run 71 of 100 1099s /usr/bin/bowtie2 --score-min L,5.976988121422,3.04997045465162 --ma 2.36597582097535 --rdg 14.5028411386262,17.0712840073086 --trim5 3 --mp 2.67150564309116,1.86654268794513 --cp-ival 1 --np 1 --cp-min 3 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1099s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1099s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '1' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1099s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '4' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1099s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '5' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1099s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '9' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1099s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '10' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1099s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '15' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1099s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '22' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1099s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '25' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1099s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '39' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1099s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '45' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1099s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '46' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1099s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '49' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1099s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '52' because it was < 2 characters long 1099s 52 reads; of these: 1099s 52 (100.00%) were unpaired; of these: 1099s 51 (98.08%) aligned 0 times 1099s 1 (1.92%) aligned exactly 1 time 1099s 0 (0.00%) aligned >1 times 1099s 1.92% overall alignment rate 1099s Read 50 alignments... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s GAG 1099s GAG 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s Processing line... 1099s --- Summary --- 1099s Read 1 reference strings 1099s Checked 1 alignments, 0 edits 1099s --------------- 1099s PASSED 1099s /usr/bin/bowtie2 --score-min L,5.976988121422,3.04997045465162 --ma 2.36597582097535 --rdg 14.5028411386262,17.0712840073086 --trim5 3 --mp 2.67150564309116,1.86654268794513 --cp-ival 1 --np 1 --cp-min 3 -f -p 2 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1099s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1099s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1099s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '1' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1099s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '4' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1099s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '5' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1099s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '9' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1099s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '10' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1099s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '15' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1099s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '22' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1099s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '25' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1099s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '49' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1099s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '52' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1099s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '39' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1099s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1099s Warning: skipping read '45' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1099s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 1099s Warning: skipping read '46' because it was < 2 characters long 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1099s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1099s 52 reads; of these: 1099s 52 (100.00%) were unpaired; of these: 1099s 51 (98.08%) aligned 0 times 1099s 1 (1.92%) aligned exactly 1 time 1099s 0 (0.00%) aligned >1 times 1099s 1.92% overall alignment rate 1099s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1099s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1099s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1099s Flattened IUPAC characters 1099s Mutating sequence Sim.pm.1 1099s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1099s Finished SNPs 1099s Finished ref gaps 1099s Finished read gaps 1099s Mutating sequence Sim.pm.2 1099s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1099s Finished SNPs 1099s Finished ref gaps 1099s Finished read gaps 1099s Mutated reference genome to subject genome 1099s SNPs introduced: 2 1099s Reference gaps introduced: 0 1099s Read gaps introduced: 0 1099s Rearrangements introduced: 0 1099s Created read sampler 1099s Sampling 91 reads 1099s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1099s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1099s parsing sequence Sim.pm.1... 1099s parsing sequence Sim.pm.2... 1099s Parsed 7 reference bases 1099s *** Run 72 of 100 1099s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --mm --local --trim3 0 --mp 2.84122655331355,1.00838969029166 --rdg 43.1001296856026,1.77251133679574 -M 3 --norc --rfg 48.343409398659,1.06484606746208 -i S,2.45870035700013,0.22326236217157 --score-min L,6.29203296165113,1.16070483190003 --n-ceil 0.54534455335433,1.30511795027881 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1099s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1100s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 1100s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1100s Read 50 alignments... 1100s 91 reads; of these: 1100s 91 (100.00%) were paired; of these: 1100s 91 (100.00%) aligned concordantly 0 times 1100s 0 (0.00%) aligned concordantly exactly 1 time 1100s 0 (0.00%) aligned concordantly >1 times 1100s ---- 1100s 91 pairs aligned concordantly 0 times; of these: 1100s 0 (0.00%) aligned discordantly 1 time 1100s ---- 1100s 91 pairs aligned 0 times concordantly or discordantly; of these: 1100s 182 mates make up the pairs; of these: 1100s 182 (100.00%) aligned 0 times 1100s 0 (0.00%) aligned exactly 1 time 1100s 0 (0.00%) aligned >1 times 1100s 0.00% overall alignment rate 1100s Read 100 alignments... 1100s Read 150 alignments... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --mm --local --trim3 0 --mp 2.84122655331355,1.00838969029166 --rdg 43.1001296856026,1.77251133679574 -M 3 --norc --rfg 48.343409398659,1.06484606746208 -i S,2.45870035700013,0.22326236217157 --score-min L,6.29203296165113,1.16070483190003 --n-ceil 0.54534455335433,1.30511795027881 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s --- Summary --- 1100s Read 1 reference strings 1100s Checked 0 alignments, 0 edits 1100s --------------- 1100s PASSED 1100s ALSO checking that bowtie2 and bowtie2-align match up 1100s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1100s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 1100s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1100s 91 reads; of these: 1100s 91 (100.00%) were paired; of these: 1100s 91 (100.00%) aligned concordantly 0 times 1100s 0 (0.00%) aligned concordantly exactly 1 time 1100s 0 (0.00%) aligned concordantly >1 times 1100s ---- 1100s 91 pairs aligned concordantly 0 times; of these: 1100s 0 (0.00%) aligned discordantly 1 time 1100s ---- 1100s 91 pairs aligned 0 times concordantly or discordantly; of these: 1100s 182 mates make up the pairs; of these: 1100s 182 (100.00%) aligned 0 times 1100s 0 (0.00%) aligned exactly 1 time 1100s 0 (0.00%) aligned >1 times 1100s 0.00% overall alignment rate 1100s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1100s Flattened IUPAC characters 1100s Mutating sequence Sim.pm.1 1100s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1100s Finished SNPs 1100s Finished ref gaps 1100s Finished read gaps 1100s Mutating sequence Sim.pm.2 1100s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1100s Finished SNPs 1100s Finished ref gaps 1100s Finished read gaps 1100s Mutated reference genome to subject genome 1100s SNPs introduced: 5 1100s Reference gaps introduced: 0 1100s Read gaps introduced: 1 1100s Rearrangements introduced: 1 1100s Created read sampler 1100s Sampling 106 reads 1100s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1100s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1100s parsing sequence Sim.pm.1... 1100s parsing sequence Sim.pm.2... 1100s Parsed 7 reference bases 1100s *** Run 73 of 100 1100s /usr/bin/bowtie2 --np 3 --nofw --score-min L,6.26959539806266,9.52857716285114 --n-ceil 1.42849078142164,0.256278443747977 --rfg 25.2051104607221,7.98169460261429 --trim5 3 --cp-ival 2 --cp-min 5 -k 4 --local --rdg 36.3195524556385,14.8235646090484 --trim3 4 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1100s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1100s Warning: skipping read '4' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1100s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1100s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1100s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 1100s Warning: skipping mate #2 of read '60' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '75' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '76' because it was < 2 characters long 1100s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 1100s Warning: skipping mate #2 of read '80' because it was < 2 characters long 1100s Read 50 alignments... 1100s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1100s Warning: skipping mate #2 of read '83' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '86' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '95' because it was < 2 characters long 1100s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 1100s Warning: skipping mate #1 of read '103' because it was < 2 characters long 1100s Read 100 alignments... 1100s 106 reads; of these: 1100s 90 (84.91%) were paired; of these: 1100s 90 (100.00%) aligned concordantly 0 times 1100s 0 (0.00%) aligned concordantly exactly 1 time 1100s 0 (0.00%) aligned concordantly >1 times 1100s ---- 1100s 90 pairs aligned concordantly 0 times; of these: 1100s 0 (0.00%) aligned discordantly 1 time 1100s ---- 1100s 90 pairs aligned 0 times concordantly or discordantly; of these: 1100s 180 mates make up the pairs; of these: 1100s 180 (100.00%) aligned 0 times 1100s 0 (0.00%) aligned exactly 1 time 1100s 0 (0.00%) aligned >1 times 1100s 16 (15.09%) were unpaired; of these: 1100s 16 (100.00%) aligned 0 times 1100s 0 (0.00%) aligned exactly 1 time 1100s 0 (0.00%) aligned >1 times 1100s 0.00% overall alignment rate 1100s Read 150 alignments... 1100s Read 200 alignments... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s Processing line... 1100s --- Summary --- 1100s Read 1 reference strings 1100s Checked 0 alignments, 0 edits 1100s --------------- 1100s PASSED 1100s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1100s /usr/bin/bowtie2 --np 3 --nofw --score-min L,6.26959539806266,9.52857716285114 --n-ceil 1.42849078142164,0.256278443747977 --rfg 25.2051104607221,7.98169460261429 --trim5 3 --cp-ival 2 --cp-min 5 -k 4 --local --rdg 36.3195524556385,14.8235646090484 --trim3 4 -f -p 4 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1101s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read '4' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1101s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1101s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1101s Warning: skipping mate #2 of read '83' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '86' because it was < 2 characters long 1101s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 1101s Warning: skipping mate #2 of read '60' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '95' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '75' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '76' because it was < 2 characters long 1101s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 1101s Warning: skipping mate #2 of read '80' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 1101s Warning: skipping mate #1 of read '103' because it was < 2 characters long 1101s 106 reads; of these: 1101s 90 (84.91%) were paired; of these: 1101s 90 (100.00%) aligned concordantly 0 times 1101s 0 (0.00%) aligned concordantly exactly 1 time 1101s 0 (0.00%) aligned concordantly >1 times 1101s ---- 1101s 90 pairs aligned concordantly 0 times; of these: 1101s 0 (0.00%) aligned discordantly 1 time 1101s ---- 1101s 90 pairs aligned 0 times concordantly or discordantly; of these: 1101s 180 mates make up the pairs; of these: 1101s 180 (100.00%) aligned 0 times 1101s 0 (0.00%) aligned exactly 1 time 1101s 0 (0.00%) aligned >1 times 1101s 16 (15.09%) were unpaired; of these: 1101s 16 (100.00%) aligned 0 times 1101s 0 (0.00%) aligned exactly 1 time 1101s 0 (0.00%) aligned >1 times 1101s 0.00% overall alignment rate 1101s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1101s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1101s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1101s Flattened IUPAC characters 1101s Mutating sequence Sim.pm.2 1101s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1101s Finished SNPs 1101s Finished ref gaps 1101s Finished read gaps 1101s Mutating sequence Sim.pm.1 1101s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1101s Finished SNPs 1101s Finished ref gaps 1101s Finished read gaps 1101s Mutated reference genome to subject genome 1101s SNPs introduced: 1 1101s Reference gaps introduced: 1 1101s Read gaps introduced: 1 1101s Rearrangements introduced: 0 1101s Created read sampler 1101s Sampling 87 reads 1101s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1101s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1101s parsing sequence Sim.pm.1... 1101s parsing sequence Sim.pm.2... 1101s Parsed 7 reference bases 1101s *** Run 74 of 100 1101s /usr/bin/bowtie2 --np 1 -D 48 --rfg 27.4027499692672,12.4459929614837 --trim5 7 --gbar 4 --score-min L,3.12989196741992,4.87114427194338 --cp-min 7 --mm --cp-ival 1 --mp 2.72564908102163,2.43476711863429 --trim3 5 --ma 1.16039808496546 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1101s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s 87 reads; of these: 1101s 87 (100.00%) were unpaired; of these: 1101s 83 (95.40%) aligned 0 times 1101s 4 (4.60%) aligned exactly 1 time 1101s 0 (0.00%) aligned >1 times 1101s 4.60% overall alignment rate 1101s Read 50 alignments... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s AGG 1101s AGG 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s GGT 1101s GGT 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s GG 1101s GG 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s GT 1101s GT 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s --- Summary --- 1101s Read 1 reference strings 1101s Checked 4 alignments, 0 edits 1101s --------------- 1101s PASSED 1101s ALSO checking that bowtie2 and bowtie2-align match up 1101s /usr/bin/bowtie2 --np 1 -D 48 --rfg 27.4027499692672,12.4459929614837 --trim5 7 --gbar 4 --score-min L,3.12989196741992,4.87114427194338 --cp-min 7 --mm --cp-ival 1 --mp 2.72564908102163,2.43476711863429 --trim3 5 --ma 1.16039808496546 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1101s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1101s 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 1101s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 1101s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 1101s 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 1101s 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 1101s 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 1101s 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 1101s 87 reads; of these: 1101s 87 (100.00%) were unpaired; of these: 1101s 83 (95.40%) aligned 0 times 1101s 4 (4.60%) aligned exactly 1 time 1101s 0 (0.00%) aligned >1 times 1101s 4.60% overall alignment rate 1101s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1101s Flattened IUPAC characters 1101s Mutating sequence Sim.pm.2 1101s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1101s Finished SNPs 1101s Finished ref gaps 1101s Finished read gaps 1101s Mutating sequence Sim.pm.1 1101s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1101s Finished SNPs 1101s Finished ref gaps 1101s Finished read gaps 1101s Mutated reference genome to subject genome 1101s SNPs introduced: 3 1101s Reference gaps introduced: 0 1101s Read gaps introduced: 0 1101s Rearrangements introduced: 0 1101s Created read sampler 1101s Sampling 19 reads 1101s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1101s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1101s parsing sequence Sim.pm.1... 1101s parsing sequence Sim.pm.2... 1101s Parsed 7 reference bases 1101s *** Run 75 of 100 1101s /usr/bin/bowtie2 --cp-min 7 --mm --cp-ival 2 --local --rdg 22.6636612067983 --trim3 8 --mp 7.91349046428068,6.89574260829861 -M 12 -N 1 -L23 --rfg 35.5395230491923,8.49632490621303 -i S,0.483434665059646 --trim5 7 --score-min L,5.23527984647024,4.11832597668176 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1101s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1101s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 1101s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (1) 1101s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 1101s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1101s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 1101s Warning: skipping read '8' because it was < 2 characters long 1101s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 1101s Warning: skipping read '9' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 1101s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1101s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 1101s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1101s 19 reads; of these: 1101s 14 (73.68%) were paired; of these: 1101s 14 (100.00%) aligned concordantly 0 times 1101s 0 (0.00%) aligned concordantly exactly 1 time 1101s 0 (0.00%) aligned concordantly >1 times 1101s ---- 1101s 14 pairs aligned concordantly 0 times; of these: 1101s 0 (0.00%) aligned discordantly 1 time 1101s ---- 1101s 14 pairs aligned 0 times concordantly or discordantly; of these: 1101s 28 mates make up the pairs; of these: 1101s 28 (100.00%) aligned 0 times 1101s 0 (0.00%) aligned exactly 1 time 1101s 0 (0.00%) aligned >1 times 1101s 5 (26.32%) were unpaired; of these: 1101s 5 (100.00%) aligned 0 times 1101s 0 (0.00%) aligned exactly 1 time 1101s 0 (0.00%) aligned >1 times 1101s 0.00% overall alignment rate 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s Processing line... 1101s --- Summary --- 1101s Read 1 reference strings 1101s Checked 0 alignments, 0 edits 1101s --------------- 1101s PASSED 1101s Flattened IUPAC characters 1101s Mutating sequence Sim.pm.2 1101s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1101s Finished SNPs 1101s Finished ref gaps 1101s Finished read gaps 1101s Mutating sequence Sim.pm.1 1101s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1101s Finished SNPs 1101s Finished ref gaps 1101s Finished read gaps 1101s Mutated reference genome to subject genome 1101s SNPs introduced: 12 1101s Reference gaps introduced: 0 1101s Read gaps introduced: 0 1101s Rearrangements introduced: 0 1101s Created read sampler 1101s Sampling 80 reads 1102s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1102s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1102s parsing sequence Sim.pm.1... 1102s parsing sequence Sim.pm.2... 1102s Parsed 7 reference bases 1102s *** Run 76 of 100 1102s /usr/bin/bowtie2 --cp-min 2 --cp-ival 5 --local --trim3 3 -k 2 -i S,1.59079748309114 --rfg 39.2171454254805,11.8491938194174 --trim5 1 --score-min L,3.70059401334752,6.31992149501728 --n-ceil 0.779679577459006,1.29804731385504 -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw 1102s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1102s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1102s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 1102s Warning: skipping mate #2 of read '21' because it was < 2 characters long 1102s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1102s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (0) 1102s Warning: skipping mate #2 of read '49' because it was < 2 characters long 1102s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 1102s Warning: skipping mate #2 of read '52' because it was < 2 characters long 1102s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1102s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1102s /usr/bin/bowtie2 --cp-min 2 --cp-ival 5 --local --trim3 3 -k 2 -i S,1.59079748309114 --rfg 39.2171454254805,11.8491938194174 --trim5 1 --score-min L,3.70059401334752,6.31992149501728 --n-ceil 0.779679577459006,1.29804731385504 -r -p 2 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1102s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '65' because it was < 2 characters long 1102s Read 50 alignments... 1102s Read 100 alignments... 1102s 80 reads; of these: 1102s 76 (95.00%) were paired; of these: 1102s 76 (100.00%) aligned concordantly 0 times 1102s 0 (0.00%) aligned concordantly exactly 1 time 1102s 0 (0.00%) aligned concordantly >1 times 1102s ---- 1102s 76 pairs aligned concordantly 0 times; of these: 1102s 0 (0.00%) aligned discordantly 1 time 1102s ---- 1102s 76 pairs aligned 0 times concordantly or discordantly; of these: 1102s 152 mates make up the pairs; of these: 1102s 152 (100.00%) aligned 0 times 1102s 0 (0.00%) aligned exactly 1 time 1102s 0 (0.00%) aligned >1 times 1102s 4 (5.00%) were unpaired; of these: 1102s 4 (100.00%) aligned 0 times 1102s 0 (0.00%) aligned exactly 1 time 1102s 0 (0.00%) aligned >1 times 1102s 0.00% overall alignment rate 1102s Read 150 alignments... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s Processing line... 1102s --- Summary --- 1102s Read 1 reference strings 1102s Checked 0 alignments, 0 edits 1102s --------------- 1102s PASSED 1102s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1102s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1102s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1102s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 1102s Warning: skipping mate #2 of read '21' because it was < 2 characters long 1102s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1102s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (0) 1102s Warning: skipping mate #2 of read '49' because it was < 2 characters long 1102s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 1102s Warning: skipping mate #2 of read '52' because it was < 2 characters long 1102s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1102s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1102s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 1102s Warning: skipping mate #1 of read '65' because it was < 2 characters long 1102s 80 reads; of these: 1102s 76 (95.00%) were paired; of these: 1102s 76 (100.00%) aligned concordantly 0 times 1102s 0 (0.00%) aligned concordantly exactly 1 time 1102s 0 (0.00%) aligned concordantly >1 times 1102s ---- 1102s 76 pairs aligned concordantly 0 times; of these: 1102s 0 (0.00%) aligned discordantly 1 time 1102s ---- 1102s 76 pairs aligned 0 times concordantly or discordantly; of these: 1102s 152 mates make up the pairs; of these: 1102s 152 (100.00%) aligned 0 times 1102s 0 (0.00%) aligned exactly 1 time 1102s 0 (0.00%) aligned >1 times 1102s 4 (5.00%) were unpaired; of these: 1102s 4 (100.00%) aligned 0 times 1102s 0 (0.00%) aligned exactly 1 time 1102s 0 (0.00%) aligned >1 times 1102s 0.00% overall alignment rate 1102s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1102s Flattened IUPAC characters 1102s Mutating sequence Sim.pm.1 1102s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1102s Finished SNPs 1102s Finished ref gaps 1102s Finished read gaps 1102s Mutating sequence Sim.pm.2 1102s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1102s Finished SNPs 1102s Finished ref gaps 1102s Finished read gaps 1102s Mutated reference genome to subject genome 1102s SNPs introduced: 1 1102s Reference gaps introduced: 0 1102s Read gaps introduced: 0 1102s Rearrangements introduced: 0 1102s Created read sampler 1102s Sampling 136 reads 1102s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1102s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1102s parsing sequence Sim.pm.1... 1102s parsing sequence Sim.pm.2... 1102s Parsed 7 reference bases 1102s *** Run 77 of 100 1102s /usr/bin/bowtie2 --n-ceil 0.366522698735087,1.24251302616373 --score-min L,3.4879517892729,8.94451584633619 -i S,1.59447240295361 --rfg 3.70945719923073,17.905756468414 --mm --cp-ival 1 --cp-min 2 -k 2 --local -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw 1103s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '21' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1103s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #1 of read '31' because it was < 2 characters long 1103s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '74' because length (1) <= # seed mismatches (0) 1103s Read 50 alignments... 1103s Warning: skipping mate #2 of read '74' because it was < 2 characters long 1103s Read 100 alignments... 1103s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '75' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '104' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '104' because it was < 2 characters long 1103s Warning: skipping mate #1 of read '118' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #1 of read '118' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '123' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '123' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '126' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '126' because it was < 2 characters long 1103s Read 150 alignments... 1103s Read 200 alignments... 1103s 136 reads; of these: 1103s 136 (100.00%) were paired; of these: 1103s 136 (100.00%) aligned concordantly 0 times 1103s 0 (0.00%) aligned concordantly exactly 1 time 1103s 0 (0.00%) aligned concordantly >1 times 1103s ---- 1103s 136 pairs aligned concordantly 0 times; of these: 1103s 0 (0.00%) aligned discordantly 1 time 1103s ---- 1103s 136 pairs aligned 0 times concordantly or discordantly; of these: 1103s 272 mates make up the pairs; of these: 1103s 272 (100.00%) aligned 0 times 1103s 0 (0.00%) aligned exactly 1 time 1103s 0 (0.00%) aligned >1 times 1103s 0.00% overall alignment rate 1103s Read 250 alignments... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s 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Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s /usr/bin/bowtie2 --n-ceil 0.366522698735087,1.24251302616373 --score-min L,3.4879517892729,8.94451584633619 -i S,1.59447240295361 --rfg 3.70945719923073,17.905756468414 --mm --cp-ival 1 --cp-min 2 -k 2 --local -r -p 3 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing 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line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s Processing line... 1103s --- Summary --- 1103s Read 1 reference strings 1103s Checked 0 alignments, 0 edits 1103s --------------- 1103s PASSED 1103s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1103s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '21' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '24' because it was < 2 characters long 1103s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #1 of read '31' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '74' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '74' because it was < 2 characters long 1103s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '75' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '104' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '104' because it was < 2 characters long 1103s Warning: skipping mate #1 of read '118' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #1 of read '118' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '123' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '123' because it was < 2 characters long 1103s Warning: skipping mate #2 of read '126' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read '126' because it was < 2 characters long 1103s 136 reads; of these: 1103s 136 (100.00%) were paired; of these: 1103s 136 (100.00%) aligned concordantly 0 times 1103s 0 (0.00%) aligned concordantly exactly 1 time 1103s 0 (0.00%) aligned concordantly >1 times 1103s ---- 1103s 136 pairs aligned concordantly 0 times; of these: 1103s 0 (0.00%) aligned discordantly 1 time 1103s ---- 1103s 136 pairs aligned 0 times concordantly or discordantly; of these: 1103s 272 mates make up the pairs; of these: 1103s 272 (100.00%) aligned 0 times 1103s 0 (0.00%) aligned exactly 1 time 1103s 0 (0.00%) aligned >1 times 1103s 0.00% overall alignment rate 1103s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1103s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1103s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1103s Flattened IUPAC characters 1103s Mutating sequence Sim.pm.1 1103s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1103s Finished SNPs 1103s Finished ref gaps 1103s Finished read gaps 1103s Mutating sequence Sim.pm.2 1103s Introducing 4 SNPs, 2/0 ref/read gaps, and 1 rearrangements 1103s Finished SNPs 1103s Finished ref gaps 1103s Finished read gaps 1103s Mutated reference genome to subject genome 1103s SNPs introduced: 4 1103s Reference gaps introduced: 3 1103s Read gaps introduced: 0 1103s Rearrangements introduced: 1 1103s Created read sampler 1103s Sampling 156 reads 1103s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1103s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1103s parsing sequence Sim.pm.1... 1103s parsing sequence Sim.pm.2... 1103s Parsed 7 reference bases 1103s *** Run 78 of 100 1103s /usr/bin/bowtie2 --rdg 19.0231594154465 --score-min L,9.1004899025623,1.3326520637029 --ma 22.2782785411243 --norc --cp-min 3 --cp-ival 1 --qseq -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.qseq -2 /tmp/Sim.pm.dpFRpda2_2.qseq 1103s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s Warning: skipping mate #2 of read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #2 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s Read 50 alignments... 1103s Read 100 alignments... 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s 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 1103s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 1103s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 1103s 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 1103s 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 1103s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s Read 150 alignments... 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s Warning: skipping mate #1 of read 'R_1_1_1_134_134_1/1' because length (1) <= # seed mismatches (0) 1104s Warning: skipping mate #1 of read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because length (1) <= # seed mismatches (0) 1104s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s Warning: skipping mate #2 of read 'R_1_1_1_148_148_1/1' because length (1) <= # seed mismatches (0) 1104s Warning: skipping mate #2 of read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s 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 1104s Read 200 alignments... 1104s 156 reads; of these: 1104s 156 (100.00%) were paired; of these: 1104s 156 (100.00%) aligned concordantly 0 times 1104s 0 (0.00%) aligned concordantly exactly 1 time 1104s 0 (0.00%) aligned concordantly >1 times 1104s ---- 1104s 156 pairs aligned concordantly 0 times; of these: 1104s 0 (0.00%) aligned discordantly 1 time 1104s ---- 1104s 156 pairs aligned 0 times concordantly or discordantly; of these: 1104s 312 mates make up the pairs; of these: 1104s 308 (98.72%) aligned 0 times 1104s 4 (1.28%) aligned exactly 1 time 1104s 0 (0.00%) aligned >1 times 1104s 1.28% overall alignment rate 1104s Read 250 alignments... 1104s Read 300 alignments... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s GG 1104s GG 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s TA 1104s TA 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s GAGGTA 1104s GAGGTA 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s GGT 1104s GGT 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s *** Run 79 of 100 1104s /usr/bin/bowtie2 --cp-min 9 --cp-ival 2 --rdg 28.6661073242403 --ma 34.6209355954917 -k 2 --np 2 -D 36 --trim5 1 -i S,1.49829969525126,0.66430017560046 --score-min L,3.98262707866882,1.15426494419226 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s --- Summary --- 1104s Read 1 reference strings 1104s Checked 4 alignments, 0 edits 1104s --------------- 1104s PASSED 1104s Flattened IUPAC characters 1104s Mutating sequence Sim.pm.1 1104s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1104s Finished SNPs 1104s Finished ref gaps 1104s Finished read gaps 1104s Mutating sequence Sim.pm.2 1104s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1104s Finished SNPs 1104s Finished ref gaps 1104s Finished read gaps 1104s Mutated reference genome to subject genome 1104s SNPs introduced: 3 1104s Reference gaps introduced: 0 1104s Read gaps introduced: 2 1104s Rearrangements introduced: 0 1104s Created read sampler 1104s Sampling 65 reads 1104s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1104s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1104s parsing sequence Sim.pm.1... 1104s parsing sequence Sim.pm.2... 1104s Parsed 7 reference bases 1104s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1104s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 1104s Warning: skipping read '5' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1104s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '30' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1104s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '31' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1104s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 1104s Warning: skipping read '33' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1104s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 1104s Warning: skipping read '51' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1104s 65 reads; of these: 1104s 65 (100.00%) were unpaired; of these: 1104s 64 (98.46%) aligned 0 times 1104s 1 (1.54%) aligned exactly 1 time 1104s 0 (0.00%) aligned >1 times 1104s 1.54% overall alignment rate 1104s Read 50 alignments... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s AG 1104s AG 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s --- Summary --- 1104s Read 1 reference strings 1104s Checked 1 alignments, 0 edits 1104s --------------- 1104s PASSED 1104s Flattened IUPAC characters 1104s Mutating sequence Sim.pm.1 1104s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1104s Finished SNPs 1104s Finished ref gaps 1104s Finished read gaps 1104s Mutating sequence Sim.pm.2 1104s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1104s Finished SNPs 1104s Finished ref gaps 1104s Finished read gaps 1104s Mutated reference genome to subject genome 1104s SNPs introduced: 9 1104s Reference gaps introduced: 0 1104s Read gaps introduced: 0 1104s Rearrangements introduced: 0 1104s Created read sampler 1104s Sampling 122 reads 1104s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1104s *** Run 80 of 100 1104s /usr/bin/bowtie2 --cp-ival 1 --cp-min 5 -k 6 --mp 9.88257962373051,5.32046523235717 --trim3 9 --rdg 6.34749523947812,3.81757497158548 --np 1 --norc --score-min L,8.48286495918572,2.06883441789585 --n-ceil 0.272011841703675,0.119821510130925 -i L,0.141120317622659,2.19416235503918 --rfg 8.21670947755701 --trim5 8 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1104s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1104s parsing sequence Sim.pm.1... 1104s parsing sequence Sim.pm.2... 1104s Parsed 7 reference bases 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1104s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '2' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1104s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1104s Warning: skipping read '4' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1104s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '5' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1104s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '6' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1104s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '7' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1104s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '8' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1104s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '10' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1104s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '11' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1104s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '12' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1104s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '13' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1104s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '14' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1104s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '16' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1104s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '17' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1104s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '18' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1104s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '19' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1104s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '21' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1104s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '23' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1104s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '24' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1104s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '25' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1104s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '29' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1104s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '31' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1104s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '32' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1104s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '36' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1104s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '37' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1104s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '38' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1104s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '40' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1104s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '41' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1104s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '43' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1104s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '44' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1104s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '45' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1104s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '46' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1104s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '49' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1104s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '50' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1104s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '51' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1104s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '52' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1104s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '58' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1104s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '59' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1104s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '63' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1104s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '64' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1104s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '69' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1104s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '73' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1104s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '76' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1104s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '78' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1104s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '79' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1104s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '80' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1104s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '84' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1104s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '85' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1104s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '87' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1104s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '88' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1104s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '90' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1104s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '92' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1104s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '98' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1104s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '100' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1104s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '103' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1104s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '106' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1104s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '107' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1104s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '108' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1104s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '110' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1104s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '117' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1104s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '119' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1104s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '120' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1104s 122 reads; of these: 1104s 122 (100.00%) were unpaired; of these: 1104s 122 (100.00%) aligned 0 times 1104s 0 (0.00%) aligned exactly 1 time 1104s 0 (0.00%) aligned >1 times 1104s 0.00% overall alignment rate 1104s Read 50 alignments... 1104s Read 100 alignments... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s /usr/bin/bowtie2 --cp-ival 1 --cp-min 5 -k 6 --mp 9.88257962373051,5.32046523235717 --trim3 9 --rdg 6.34749523947812,3.81757497158548 --np 1 --norc --score-min L,8.48286495918572,2.06883441789585 --n-ceil 0.272011841703675,0.119821510130925 -i L,0.141120317622659,2.19416235503918 --rfg 8.21670947755701 --trim5 8 -f -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s Processing line... 1104s --- Summary --- 1104s Read 1 reference strings 1104s Checked 0 alignments, 0 edits 1104s --------------- 1104s PASSED 1104s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1104s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '2' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1104s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 1104s Warning: skipping read '4' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1104s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '5' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1104s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '6' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1104s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '7' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1104s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '8' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1104s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '10' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1104s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '11' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1104s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '12' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1104s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '13' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1104s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '14' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1104s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '16' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1104s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '17' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1104s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '18' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1104s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '19' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1104s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '21' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1104s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '23' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1104s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '24' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1104s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '25' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1104s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '29' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1104s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '31' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1104s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '32' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1104s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '36' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1104s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '37' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1104s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '38' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1104s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '40' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1104s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '41' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1104s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '43' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1104s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '44' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1104s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '45' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1104s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '46' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1104s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '49' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1104s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '50' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1104s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '51' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1104s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '52' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1104s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '58' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1104s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '59' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1104s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '63' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1104s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '64' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1104s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '69' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1104s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '73' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1104s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '76' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1104s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '78' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1104s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '79' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1104s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '80' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1104s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '84' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1104s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '85' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1104s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '87' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1104s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '88' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1104s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '90' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1104s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '92' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1104s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '98' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1104s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '100' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1104s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '103' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1104s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '106' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1104s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '107' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1104s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '108' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1104s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '110' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1104s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '117' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1104s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '119' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1104s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 1104s Warning: skipping read '120' because it was < 2 characters long 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1104s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1104s 122 reads; of these: 1104s 122 (100.00%) were unpaired; of these: 1104s 122 (diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1104s 100.00%) aligned 0 times 1104s 0 (0.00%) aligned exactly 1 time 1104s 0 (0.00%) aligned >1 times 1104s 0.00% overall alignment rate 1104s Flattened IUPAC characters 1104s Mutating sequence Sim.pm.2 1104s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1104s Finished SNPs 1104s Finished ref gaps 1104s Finished read gaps 1104s Mutating sequence Sim.pm.1 1104s Introducing 2 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1104s Finished SNPs 1104s Finished ref gaps 1104s Finished read gaps 1104s Mutated reference genome to subject genome 1104s SNPs introduced: 3 1104s Reference gaps introduced: 1 1104s Read gaps introduced: 0 1104s Rearrangements introduced: 1 1104s Created read sampler 1104s Sampling 151 reads 1104s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1104s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1104s parsing sequence Sim.pm.1... 1104s parsing sequence Sim.pm.2... 1104s Parsed 7 reference bases 1104s *** Run 81 of 100 1104s /usr/bin/bowtie2 --cp-ival 2 --cp-min 2 --local --mp 8.31605024350075,4.98650469065313 --trim3 8 -a --nofw --score-min L,5.91182821779763,1.60861640038546 --gbar 11 --rfg 18.7335830569987 -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw 1105s Warning: skipping mate #1 of read '0' because length (1) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '0' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1105s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1105s Warning: skipping read '25' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1105s Warning: skipping mate #2 of read '44' because it was < 2 characters long 1105s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 1105s Warning: skipping mate #2 of read '51' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1105s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 1105s Warning: skipping mate #2 of read '57' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1105s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 1105s Warning: skipping read '76' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '79' because it was < 2 characters long 1105s Read 50 alignments... 1105s Read 100 alignments... 1105s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '92' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '93' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '99' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '101' because it was < 2 characters long 1105s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 1105s Warning: skipping read '102' because it was < 2 characters long 1105s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1105s Warning: skipping read '104' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '105' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '117' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '129' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '132' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '138' because it was < 2 characters long 1105s 151 reads; of these: 1105s 125 (82.78%) were paired; of these: 1105s 125 (100.00%) aligned concordantly 0 times 1105s 0 (0.00%) aligned concordantly exactly 1 time 1105s 0 (0.00%) aligned concordantly >1 times 1105s ---- 1105s 125 pairs aligned concordantly 0 times; of these: 1105s 0 (0.00%) aligned discordantly 1 time 1105s ---- 1105s 125 pairs aligned 0 times concordantly or discordantly; of these: 1105s 250 mates make up the pairs; of these: 1105s 250 (100.00%) aligned 0 times 1105s 0 (0.00%) aligned exactly 1 time 1105s 0 (0.00%) aligned >1 times 1105s 26 (17.22%) were unpaired; of these: 1105s 26 (100.00%) aligned 0 times 1105s 0 (0.00%) aligned exactly 1 time 1105s 0 (0.00%) aligned >1 times 1105s 0.00% overall alignment rate 1105s Read 150 alignments... 1105s Read 200 alignments... 1105s Read 250 alignments... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s Processing line... 1105s 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Processing line... 1105s --- Summary --- 1105s /usr/bin/bowtie2 --cp-ival 2 --cp-min 2 --local --mp 8.31605024350075,4.98650469065313 --trim3 8 -a --nofw --score-min L,5.91182821779763,1.60861640038546 --gbar 11 --rfg 18.7335830569987 -r -p 4 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1105s Read 1 reference strings 1105s Checked 0 alignments, 0 edits 1105s --------------- 1105s PASSED 1105s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1105s Warning: skipping mate #1 of read '0' because length (1) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '0' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1105s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1105s Warning: skipping read '25' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1105s Warning: skipping mate #2 of read '44' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '99' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '101' because it was < 2 characters long 1105s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 1105s Warning: skipping read '102' because it was < 2 characters long 1105s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1105s Warning: skipping read '104' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '105' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '117' because it was < 2 characters long 1105s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 1105s Warning: skipping mate #2 of read '51' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1105s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 1105s Warning: skipping mate #2 of read '57' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '70' because it was < 2 characters long 1105s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 1105s Warning: skipping read '76' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '79' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '129' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '132' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '138' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '92' because it was < 2 characters long 1105s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 1105s Warning: skipping mate #1 of read '93' because it was < 2 characters long 1105s 151 reads; of these: 1105s 125 (82.78%) were paired; of these: 1105s 125 (100.00%) aligned concordantly 0 times 1105s 0 (0.00%) aligned concordantly exactly 1 time 1105s 0 (0.00%) aligned concordantly >1 times 1105s ---- 1105s 125 pairs aligned concordantly 0 times; of these: 1105s 0 (0.00%) aligned discordantly 1 time 1105s ---- 1105s 125 pairs aligned 0 times concordantly or discordantly; of these: 1105s 250 mates make up the pairs; of these: 1105s 250 (100.00%) aligned 0 times 1105s 0 (0.00%) aligned exactly 1 time 1105s 0 (0.00%) aligned >1 times 1105s 26 (17.22%) were unpaired; of these: 1105s 26 (100.00%) aligned 0 times 1105s 0 (0.00%) aligned exactly 1 time 1105s 0 (0.00%) aligned >1 times 1105s 0.00% overall alignment rate 1105s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1105s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1105s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1105s Flattened IUPAC characters 1105s Mutating sequence Sim.pm.2 1105s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1105s Finished SNPs 1105s Finished ref gaps 1105s Finished read gaps 1105s Mutating sequence Sim.pm.1 1105s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1105s Finished SNPs 1105s Finished ref gaps 1105s Finished read gaps 1105s Mutated reference genome to subject genome 1105s SNPs introduced: 8 1105s Reference gaps introduced: 0 1105s Read gaps introduced: 0 1105s Rearrangements introduced: 0 1105s Created read sampler 1105s Sampling 130 reads 1105s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1105s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1105s parsing sequence Sim.pm.1... 1105s parsing sequence Sim.pm.2... 1105s *** Run 82 of 100 1105s /usr/bin/bowtie2 -N 0 -L22 --mm --cp-ival 1 --cp-min 2 --np 1 --n-ceil 0.1868779947444,0.937609226068847 --score-min L,8.08291563161082,6.24541954922521 --trim5 3 -a --local -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw 1105s Parsed 7 reference bases 1106s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '61' because length (1) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '76' because it was < 2 characters long 1106s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 1106s Warning: skipping read '79' because it was < 2 characters long 1106s Read 50 alignments... 1106s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '82' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1106s Read 100 alignments... 1106s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '109' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '124' because it was < 2 characters long 1106s Read 150 alignments... 1106s Read 200 alignments... 1106s 130 reads; of these: 1106s 124 (95.38%) were paired; of these: 1106s 124 (100.00%) aligned concordantly 0 times 1106s 0 (0.00%) aligned concordantly exactly 1 time 1106s 0 (0.00%) aligned concordantly >1 times 1106s ---- 1106s 124 pairs aligned concordantly 0 times; of these: 1106s 0 (0.00%) aligned discordantly 1 time 1106s ---- 1106s 124 pairs aligned 0 times concordantly or discordantly; of these: 1106s 248 mates make up the pairs; of these: 1106s 248 (100.00%) aligned 0 times 1106s 0 ( Read 250 alignments... 1106s 0.00%) aligned exactly 1 time 1106s 0 (0.00%) aligned >1 times 1106s 6 (4.62%) were unpaired; of these: 1106s 6 (100.00%) aligned 0 times 1106s 0 (0.00%) aligned exactly 1 time 1106s 0 (0.00%) aligned >1 times 1106s 0.00% overall alignment rate 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s 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Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s --- Summary --- 1106s Read 1 reference strings 1106s Checked 0 alignments, 0 edits 1106s --------------- 1106s PASSED 1106s ALSO checking that bowtie2 and bowtie2-align match up 1106s /usr/bin/bowtie2 -N 0 -L22 --mm --cp-ival 1 --cp-min 2 --np 1 --n-ceil 0.1868779947444,0.937609226068847 --score-min L,8.08291563161082,6.24541954922521 --trim5 3 -a --local -r -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.raw -2 /tmp/Sim.pm.dpFRpda2_2.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1106s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '61' because length (1) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '76' because it was < 2 characters long 1106s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 1106s Warning: skipping read '79' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '82' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '109' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1106s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 1106s Warning: skipping mate #1 of read '124' because it was < 2 characters long 1106s 130 reads; of these: 1106s 124 (95.38%) were paired; of these: 1106s 124 (100.00%) aligned concordantly 0 times 1106s 0 (0.00%) aligned concordantly exactly 1 time 1106s 0 (0.00%) aligned concordantly >1 times 1106s ---- 1106s 124 pairs aligned concordantly 0 times; of these: 1106s 0 (0.00%) aligned discordantly 1 time 1106s ---- 1106s 124 pairs aligned 0 times concordantly or discordantly; of these: 1106s 248 mates make up the pairs; of these: 1106s 248 (100.00%) aligned 0 times 1106s 0 (0.00%) aligned exactly 1 time 1106s 0 (0.00%) aligned >1 times 1106s 6 (4.62%) were unpaired; of these: 1106s 6 (100.00%) aligned 0 times 1106s 0 (0.00%) aligned exactly 1 time 1106s 0 (0.00%) aligned >1 times 1106s 0.00% overall alignment rate 1106s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1106s Flattened IUPAC characters 1106s Mutating sequence Sim.pm.1 1106s Introducing 2 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1106s Finished SNPs 1106s Finished ref gaps 1106s Finished read gaps 1106s Mutating sequence Sim.pm.2 1106s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1106s Finished SNPs 1106s Finished ref gaps 1106s Finished read gaps 1106s Mutated reference genome to subject genome 1106s SNPs introduced: 2 1106s Reference gaps introduced: 1 1106s Read gaps introduced: 1 1106s Rearrangements introduced: 1 1106s Created read sampler 1106s Sampling 135 reads 1106s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1106s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1106s parsing sequence Sim.pm.1... 1106s parsing sequence Sim.pm.2... 1106s Parsed 7 reference bases 1106s *** Run 83 of 100 1106s /usr/bin/bowtie2 --cp-min 4 --nofw -N 1 -L27 --cp-ival 2 --mm --mp 5.60646256084988,2.6022964796029 --rdg 3.73636106336056,16.9664970064313 --local --score-min L,9.24667088220223,8.33060828554524 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1106s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '8' because it was < 2 characters long 1106s Warning: skipping read '11' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '11' because it was < 2 characters long 1106s Warning: skipping read '37' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '37' because it was < 2 characters long 1106s Warning: skipping read '40' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '40' because it was < 2 characters long 1106s Warning: skipping read '64' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '64' because it was < 2 characters long 1106s Warning: skipping read '69' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '69' because it was < 2 characters long 1106s Warning: skipping read '99' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '99' because it was < 2 characters long 1106s 135 reads; of these: 1106s 135 (100.00%) were unpaired; of these: 1106s 135 (100.00%) aligned 0 times 1106s 0 (0.00%) aligned exactly 1 time 1106s 0 (0.00%) aligned >1 times 1106s 0.00% overall alignment rate 1106s Read 50 alignments... 1106s Read 100 alignments... 1106s Processing line... 1106s Processing line... 1106s /usr/bin/bowtie2 --cp-min 4 --nofw -N 1 -L27 --cp-ival 2 --mm --mp 5.60646256084988,2.6022964796029 --rdg 3.73636106336056,16.9664970064313 --local --score-min L,9.24667088220223,8.33060828554524 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s 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Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s Processing line... 1106s --- Summary --- 1106s Read 1 reference strings 1106s Checked 0 alignments, 0 edits 1106s --------------- 1106s PASSED 1106s ALSO checking that bowtie2 and bowtie2-align match up 1106s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '8' because it was < 2 characters long 1106s Warning: skipping read '11' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '11' because it was < 2 characters long 1106s Warning: skipping read '37' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '37' because it was < 2 characters long 1106s Warning: skipping read '40' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '40' because it was < 2 characters long 1106s Warning: skipping read '64' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '64' because it was < 2 characters long 1106s Warning: skipping read '69' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '69' because it was < 2 characters long 1106s Warning: skipping read '99' because length (1) <= # seed mismatches (1) 1106s Warning: skipping read '99' because it was < 2 characters long 1106s 135 reads; of these: 1106s 135 (100.00%) were unpaired; of these: 1106s 135 (100.00%) aligned 0 times 1106s 0 (0.00%) aligned exactly 1 time 1106s 0 (0.00%) aligned >1 times 1106s 0.00% overall alignment rate 1106s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1106s /usr/bin/bowtie2 --cp-min 4 --nofw -N 1 -L27 --cp-ival 2 --mm --mp 5.60646256084988,2.6022964796029 --rdg 3.73636106336056,16.9664970064313 --local --score-min L,9.24667088220223,8.33060828554524 -f -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1106s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1107s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 1107s Warning: skipping read '8' because it was < 2 characters long 1107s Warning: skipping read '11' because length (1) <= # seed mismatches (1) 1107s Warning: skipping read '11' because it was < 2 characters long 1107s Warning: skipping read '37' because length (1) <= # seed mismatches (1) 1107s Warning: skipping read '37' because it was < 2 characters long 1107s Warning: skipping read '40' because length (1) <= # seed mismatches (1) 1107s Warning: skipping read '40' because it was < 2 characters long 1107s Warning: skipping read '69' because length (1) <= # seed mismatches (1) 1107s Warning: skipping read '69' because it was < 2 characters long 1107s Warning: skipping read '64' because length (1) <= # seed mismatches (1) 1107s Warning: skipping read '64' because it was < 2 characters long 1107s Warning: skipping read '99' because length (1) <= # seed mismatches (1) 1107s Warning: skipping read '99' because it was < 2 characters long 1107s 135 reads; of these: 1107s 135 (100.00%) were unpaired; of these: 1107s 135 (100.00%) aligned 0 times 1107s 0 (0.00%) aligned exactly 1 time 1107s 0 (0.00%) aligned >1 times 1107s 0.00% overall alignment rate 1107s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1107s Flattened IUPAC characters 1107s Mutating sequence Sim.pm.2 1107s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1107s Finished SNPs 1107s Finished ref gaps 1107s Finished read gaps 1107s Mutating sequence Sim.pm.1 1107s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1107s Finished SNPs 1107s Finished ref gaps 1107s Finished read gaps 1107s Mutated reference genome to subject genome 1107s SNPs introduced: 3 1107s Reference gaps introduced: 0 1107s Read gaps introduced: 0 1107s Rearrangements introduced: 1 1107s Created read sampler 1107s Sampling 71 reads 1107s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1107s *** Run 84 of 100 1107s /usr/bin/bowtie2 --ma 38.3928406668787 -a --mm --cp-ival 2 --cp-min 3 --n-ceil 0.921971966450856,0.0981775067490936 --score-min L,8.27329072972281,3.62611149680776 --rfg 34.7766140201186,4.29122726561237 -R 3 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1107s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1107s parsing sequence Sim.pm.1... 1107s parsing sequence Sim.pm.2... 1107s Parsed 7 reference bases 1107s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 71 reads; of these: 1107s 71 (100.00%) were unpaired; of these: 1107s 67 (94.37%) aligned 0 times 1107s 4 (5.63%) aligned exactly 1 time 1107s 0 (0.00%) aligned >1 times 1107s 5.63% overall alignment rate 1107s Read 50 alignments... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s AGG 1107s AGG 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s AG 1107s AG 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s GG 1107s GG 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s GT 1107s GT 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s --- Summary --- 1107s Read 1 reference strings 1107s Checked 4 alignments, 0 edits 1107s --------------- 1107s PASSED 1107s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1107s /usr/bin/bowtie2 --ma 38.3928406668787 -a --mm --cp-ival 2 --cp-min 3 --n-ceil 0.921971966450856,0.0981775067490936 --score-min L,8.27329072972281,3.62611149680776 --rfg 34.7766140201186,4.29122726561237 -R 3 --qseq -p 2 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1107s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 71 reads; of these: 1107s 71 (100.00%) were unpaired; of these: 1107s 67 (94.37%) aligned 0 times 1107s 4 (5.63%) aligned exactly 1 time 1107s 0 (0.00%) aligned >1 times 1107s 5.63% overall alignment rate 1107s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1107s Flattened IUPAC characters 1107s Mutating sequence Sim.pm.2 1107s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1107s Finished SNPs 1107s Finished ref gaps 1107s Finished read gaps 1107s Mutating sequence Sim.pm.1 1107s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1107s Finished SNPs 1107s Finished ref gaps 1107s Finished read gaps 1107s Mutated reference genome to subject genome 1107s SNPs introduced: 5 1107s Reference gaps introduced: 0 1107s Read gaps introduced: 1 1107s Rearrangements introduced: 0 1107s Created read sampler 1107s Sampling 80 reads 1107s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1107s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1107s parsing sequence Sim.pm.1... 1107s parsing sequence Sim.pm.2... 1107s Parsed 7 reference bases 1107s *** Run 85 of 100 1107s /usr/bin/bowtie2 --cp-ival 2 --cp-min 3 -k 4 --trim3 2 --mp 9.86797686423084,8.46825788300574 --rdg 37.8106069666807,3.45012294420062 --score-min L,6.64593375423195,3.20501720412935 --gbar 4 --n-ceil 0.758662282017197,1.2175779745421 --rfg 9.58669550477952 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1107s 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 1107s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 1107s 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 1107s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1107s 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 1107s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 1107s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 1107s 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 1107s 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 1107s 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 1107s 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 1107s 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 1107s 80 reads; of these: 1107s 80 (100.00%) were unpaired; of these: 1107s 79 (98.75%) aligned 0 times 1107s 1 (1.25%) aligned exactly 1 time 1107s 0 (0.00%) aligned >1 times 1107s 1.25% overall alignment rate 1107s Read 50 alignments... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s AGGT 1107s AGGT 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s Processing line... 1107s --- Summary --- 1107s Read 1 reference strings 1107s Checked 1 alignments, 0 edits 1107s --------------- 1107s PASSED 1107s Flattened IUPAC characters 1107s Mutating sequence Sim.pm.1 1107s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1107s Finished SNPs 1107s Finished ref gaps 1107s Finished read gaps 1107s Mutating sequence Sim.pm.2 1107s Introducing 2 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1107s Finished SNPs 1107s Finished ref gaps 1107s Finished read gaps 1107s Mutated reference genome to subject genome 1107s SNPs introduced: 3 1107s Reference gaps introduced: 1 1107s Read gaps introduced: 1 1107s Rearrangements introduced: 2 1107s Created read sampler 1107s Sampling 91 reads 1107s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.qseq & /tmp/Sim.pm.dpFRpda2_2.qseq 1107s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1107s parsing sequence Sim.pm.1... 1107s parsing sequence Sim.pm.2... 1107s Parsed 7 reference bases 1107s *** Run 86 of 100 1107s /usr/bin/bowtie2 --cp-ival 1 --cp-min 4 --mp 9.24840967455638,5.83502249325482 --local --norc --gbar 2 --score-min L,3.34357894966575,3.36615079134834 --qseq -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq 1108s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 1108s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1108s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 1108s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1108s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 1108s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1108s 91 reads; of these: 1108s 91 (100.00%) were unpaired; of these: 1108s 91 (100.00%) aligned 0 times 1108s 0 (0.00%) aligned exactly 1 time 1108s 0 (0.00%) aligned >1 times 1108s 0.00% overall alignment rate 1108s Read 50 alignments... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s /usr/bin/bowtie2 --cp-ival 1 --cp-min 4 --mp 9.24840967455638,5.83502249325482 --local --norc --gbar 2 --score-min L,3.34357894966575,3.36615079134834 --qseq -p 4 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s --- Summary --- 1108s Read 1 reference strings 1108s Checked 0 alignments, 0 edits 1108s --------------- 1108s PASSED 1108s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1108s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 1108s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1108s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 1108s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1108s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 1108s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1108s 91 reads; of these: 1108s 91 (100.00%) were unpaired; of these: 1108s 91 (100.00%) aligned 0 times 1108s 0 (0.00%) aligned exactly 1 time 1108s 0 (0.00%) aligned >1 times 1108s 0.00% overall alignment rate 1108s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1108s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1108s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1108s Flattened IUPAC characters 1108s Mutating sequence Sim.pm.2 1108s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1108s Finished SNPs 1108s Finished ref gaps 1108s Finished read gaps 1108s Mutating sequence Sim.pm.1 1108s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1108s Finished SNPs 1108s Finished ref gaps 1108s Finished read gaps 1108s Mutated reference genome to subject genome 1108s SNPs introduced: 0 1108s Reference gaps introduced: 0 1108s Read gaps introduced: 0 1108s Rearrangements introduced: 0 1108s Created read sampler 1108s Sampling 20 reads 1108s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1108s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1108s parsing sequence Sim.pm.1... 1108s parsing sequence Sim.pm.2... 1108s Parsed 7 reference bases 1108s *** Run 87 of 100 1108s /usr/bin/bowtie2 -M 4 --rdg 4.08735833662816,13.7497669266212 --mp 8.96764552046073,4.33592160816926 --local --mm --cp-ival 1 --cp-min 11 --score-min L,9.37582055895811,9.92719937107151 --trim5 0 -i S,1.38529553858103 --np 4 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1108s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1108s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 1108s Warning: skipping mate #2 of read '8' because it was < 2 characters long 1108s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 1108s Warning: skipping mate #2 of read '18' because it was < 2 characters long 1108s 20 reads; of these: 1108s 20 (100.00%) were paired; of these: 1108s 20 (100.00%) aligned concordantly 0 times 1108s 0 (0.00%) aligned concordantly exactly 1 time 1108s 0 (0.00%) aligned concordantly >1 times 1108s ---- 1108s 20 pairs aligned concordantly 0 times; of these: 1108s 0 (0.00%) aligned discordantly 1 time 1108s ---- 1108s 20 pairs aligned 0 times concordantly or discordantly; of these: 1108s 40 mates make up the pairs; of these: 1108s 40 (100.00%) aligned 0 times 1108s 0 (0.00%) aligned exactly 1 time 1108s 0 (0.00%) aligned >1 times 1108s 0.00% overall alignment rate 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s Processing line... 1108s --- Summary --- 1108s Read 1 reference strings 1108s Checked 0 alignments, 0 edits 1108s --------------- 1108s PASSED 1108s ALSO checking that bowtie2 and bowtie2-align match up 1108s /usr/bin/bowtie2 -M 4 --rdg 4.08735833662816,13.7497669266212 --mp 8.96764552046073,4.33592160816926 --local --mm --cp-ival 1 --cp-min 11 --score-min L,9.37582055895811,9.92719937107151 --trim5 0 -i S,1.38529553858103 --np 4 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1108s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1108s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 1108s Warning: skipping mate #2 of read '8' because it was < 2 characters long 1108s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 1108s Warning: skipping mate #2 of read '18' because it was < 2 characters long 1108s 20 reads; of these: 1108s 20 (100.00%) were paired; of these: 1108s 20 (100.00%) aligned concordantly 0 times 1108s 0 (0.00%) aligned concordantly exactly 1 time 1108s 0 (0.00%) aligned concordantly >1 times 1108s ---- 1108s 20 pairs aligned concordantly 0 times; of these: 1108s 0 (0.00%) aligned discordantly 1 time 1108s ---- 1108s 20 pairs aligned 0 times concordantly or discordantly; of these: 1108s 40 mates make up the pairs; of these: 1108s 40 (100.00%) aligned 0 times 1108s 0 (0.00%) aligned exactly 1 time 1108s 0 (0.00%) aligned >1 times 1108s 0.00% overall alignment rate 1108s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1109s Flattened IUPAC characters 1109s Mutating sequence Sim.pm.2 1109s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1109s Finished SNPs 1109s Finished ref gaps 1109s Finished read gaps 1109s Mutating sequence Sim.pm.1 1109s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1109s Finished SNPs 1109s Finished ref gaps 1109s Finished read gaps 1109s Mutated reference genome to subject genome 1109s SNPs introduced: 1 1109s Reference gaps introduced: 0 1109s Read gaps introduced: 0 1109s Rearrangements introduced: 1 1109s Created read sampler 1109s Sampling 44 reads 1109s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1109s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1109s parsing sequence Sim.pm.1... 1109s parsing sequence Sim.pm.2... 1109s Parsed 7 reference bases 1109s *** Run 88 of 100 1109s /usr/bin/bowtie2 --cp-min 5 --cp-ival 2 -D 45 -R 2 --mm --mp 5.62762232839498,3.58832981530951 -M 2 --ma 30.8851803411917 --score-min L,8.2329511553053,4.20269483943892 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1109s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1109s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1109s 44 reads; of these: 1109s 44 (100.00%) were paired; of these: 1109s 44 (100.00%) aligned concordantly 0 times 1109s 0 (0.00%) aligned concordantly exactly 1 time 1109s 0 (0.00%) aligned concordantly >1 times 1109s ---- 1109s 44 pairs aligned concordantly 0 times; of these: 1109s 0 (0.00%) aligned discordantly 1 time 1109s ---- 1109s 44 pairs aligned 0 times concordantly or discordantly; of these: 1109s 88 mates make up the pairs; of these: 1109s 86 (97.73%) aligned 0 times 1109s 2 (2.27%) aligned exactly 1 time 1109s 0 (0.00%) aligned >1 times 1109s 2.27% overall alignment rate 1109s Read 50 alignments... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s GAG 1109s GAG 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s /usr/bin/bowtie2 --cp-min 5 --cp-ival 2 -D 45 -R 2 --mm --mp 5.62762232839498,3.58832981530951 -M 2 --ma 30.8851803411917 --score-min L,8.2329511553053,4.20269483943892 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s GG 1109s GG 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s Processing line... 1109s --- Summary --- 1109s Read 1 reference strings 1109s Checked 2 alignments, 0 edits 1109s --------------- 1109s PASSED 1109s ALSO checking that bowtie2 and bowtie2-align match up 1109s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1109s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1109s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1109s 44 reads; of these: 1109s 44 (100.00%) were paired; of these: 1109s 44 (100.00%) aligned concordantly 0 times 1109s 0 (0.00%) aligned concordantly exactly 1 time 1109s 0 (0.00%) aligned concordantly >1 times 1109s ---- 1109s 44 pairs aligned concordantly 0 times; of these: 1109s 0 (0.00%) aligned discordantly 1 time 1109s ---- 1109s 44 pairs aligned 0 times concordantly or discordantly; of these: 1109s 88 mates make up the pairs; of these: 1109s 86 (97.73%) aligned 0 times 1109s 2 (2.27%) aligned exactly 1 time 1109s 0 (0.00%) aligned >1 times 1109s 2.27% overall alignment rate 1109s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1109s Flattened IUPAC characters 1109s Mutating sequence Sim.pm.1 1109s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1109s Finished SNPs 1109s Finished ref gaps 1109s Finished read gaps 1109s Mutating sequence Sim.pm.2 1109s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1109s Finished SNPs 1109s Finished ref gaps 1109s Finished read gaps 1109s Mutated reference genome to subject genome 1109s SNPs introduced: 6 1109s Reference gaps introduced: 1 1109s Read gaps introduced: 0 1109s Rearrangements introduced: 0 1109s Created read sampler 1109s Sampling 137 reads 1109s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1109s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1109s parsing sequence Sim.pm.1... 1109s parsing sequence Sim.pm.2... 1109s Parsed 7 reference bases 1109s *** Run 89 of 100 1109s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --rfg 12.7879334967464 --mp 9.92789462901235,3.32281008476338 -a --trim5 2 --score-min L,4.27794738888067,8.26096417251134 --ma 19.862002161923 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1110s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1110s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #2 of read '4' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1110s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1110s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1110s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1110s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '21' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1110s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1110s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1110s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #2 of read '48' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1110s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1110s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '64' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1110s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '65' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1110s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '75' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1110s Read 50 alignments... 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1110s Warning: skipping mate #1 of read '115' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '115' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1110s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 1110s Read 100 alignments... 1110s Read 150 alignments... 1110s Read 200 alignments... 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 1110s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '130' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 1110s Warning: skipping mate #1 of read '132' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '132' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 1110s Warning: skipping mate #2 of read '135' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #2 of read '135' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 1110s 137 reads; of these: 1110s 129 (94.16%) were paired; of these: 1110s 129 (100.00%) aligned concordantly 0 times 1110s 0 (0.00%) aligned concordantly exactly 1 time 1110s 0 (0.00%) aligned concordantly >1 times 1110s ---- 1110s 129 pairs aligned concordantly 0 times; of these: 1110s 0 (0.00%) aligned discordantly 1 time 1110s ---- 1110s 129 pairs aligned 0 times concordantly or discordantly; of these: 1110s 258 mates make up the pairs; of these: 1110s 249 (96.51%) aligned 0 times 1110s 9 (3.49%) aligned exactly 1 time 1110s 0 (0.00%) aligned >1 times 1110s 8 (5.84%) were unpaired; of these: 1110s 7 (87.50%) aligned 0 times 1110s 1 (12.50%) aligned exactly 1 time 1110s 0 (0.00%) aligned >1 times 1110s 3.76% overall alignment rate 1110s Read 250 alignments... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s GT 1110s GT 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s GAGG 1110s GAGG 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s GG 1110s GG 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s AGG 1110s AGG 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s GT 1110s GT 1110s Processing line... 1110s Processing line... 1110s GAGG 1110s GAGG 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s GGT 1110s GGT 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s GTA 1110s GTA 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s GAGGTA 1110s GAGGTA 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s AG 1110s AG 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s --- Summary --- 1110s Read 1 reference strings 1110s Checked 10 alignments, 0 edits 1110s --------------- 1110s PASSED 1110s Flattened IUPAC characters 1110s Mutating sequence Sim.pm.1 1110s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1110s Finished SNPs 1110s Finished ref gaps 1110s Finished read gaps 1110s Mutating sequence Sim.pm.2 1110s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1110s Finished SNPs 1110s Finished ref gaps 1110s Finished read gaps 1110s Mutated reference genome to subject genome 1110s SNPs introduced: 2 1110s Reference gaps introduced: 0 1110s Read gaps introduced: 0 1110s Rearrangements introduced: 0 1110s Created read sampler 1110s Sampling 95 reads 1110s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1110s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1110s parsing sequence Sim.pm.1... 1110s parsing sequence Sim.pm.2... 1110s Parsed 7 reference bases 1110s *** Run 90 of 100 1110s /usr/bin/bowtie2 --cp-ival 1 --cp-min 6 -k 4 --ma 39.9521776069585 --rdg 19.7204467771752,1.95681080982504 --trim3 5 --nofw --score-min L,3.93379186250843,6.19231472553068 -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1110s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1110s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1110s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1110s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1110s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1110s Warning: skipping read '23' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1110s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1110s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1110s Warning: skipping read '39' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1110s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1110s Warning: skipping read '52' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1110s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1110s Warning: skipping read '53' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1110s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1110s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1110s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1110s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1110s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '77' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1110s Read 50 alignments... 1110s Read 100 alignments... 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1110s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '82' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1110s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1110s 95 reads; of these: 1110s 82 (86.32%) were paired; of these: 1110s 82 (100.00%) aligned concordantly 0 times 1110s 0 (0.00%) aligned concordantly exactly 1 time 1110s 0 (0.00%) aligned concordantly >1 times 1110s ---- 1110s 82 pairs aligned concordantly 0 times; of these: 1110s 0 (0.00%) aligned discordantly 1 time 1110s ---- 1110s 82 pairs aligned 0 times concordantly or discordantly; of these: 1110s 164 mates make up the pairs; of these: 1110s 159 (96.95%) aligned 0 times 1110s 5 (3.05%) aligned exactly 1 time 1110s 0 (0.00%) aligned >1 times 1110s 13 (13.68%) were unpaired; of these: 1110s 13 (100.00%) aligned 0 times 1110s 0 (0.00%) aligned exactly 1 time 1110s 0 (0.00%) aligned >1 times 1110s 2.82% overall alignment rate 1110s Read 150 alignments... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s GTA 1110s GTA 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s GG 1110s GG 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s AGGT 1110s AGGT 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s GGT 1110s GGT 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s AG 1110s AG 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s Processing line... 1110s --- Summary --- 1110s Read 1 reference strings 1110s Checked 5 alignments, 0 edits 1110s --------------- 1110s PASSED 1110s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1110s /usr/bin/bowtie2 --cp-ival 1 --cp-min 6 -k 4 --ma 39.9521776069585 --rdg 19.7204467771752,1.95681080982504 --trim3 5 --nofw --score-min L,3.93379186250843,6.19231472553068 -f -p 2 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1110s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1110s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1110s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1110s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '16' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1110s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1110s Warning: skipping read '23' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1110s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1110s Warning: skipping read '52' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1110s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1110s Warning: skipping read '53' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1110s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1110s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1110s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1110s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1110s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1110s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1110s Warning: skipping read '39' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1110s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '77' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1110s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '82' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1110s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1110s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1110s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1110s 95 reads; of these: 1110s 82 (86.32%) were paired; of these: 1110s 82 (100.00%) aligned concordantly 0 times 1110s 0 (0.00%) aligned concordantly exactly 1 time 1110s 0 (0.00%) aligned concordantly >1 times 1110s ---- 1110s 82 pairs aligned concordantly 0 times; of these: 1110s 0 (0.00%) aligned discordantly 1 time 1110s ---- 1110s 82 pairs aligned 0 times concordantly or discordantly; of these: 1110s 164 mates make up the pairs; of these: 1110s 159 (96.95%) aligned 0 times 1110s 5 (3.05%) aligned exactly 1 time 1110s 0 (0.00%) aligned >1 times 1110s 13 (13.68%) were unpaired; of these: 1110s 13 (100.00%) aligned 0 times 1110s 0 (0.00%) aligned exactly 1 time 1110s 0 (0.00%) aligned >1 times 1110s 2.82% overall alignment rate 1110s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1110s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1110s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1110s Flattened IUPAC characters 1110s Mutating sequence Sim.pm.1 1110s Introducing 3 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1110s Finished SNPs 1110s Finished ref gaps 1110s Finished read gaps 1110s Mutating sequence Sim.pm.2 1110s Introducing 0 SNPs, 0/0 ref/read gaps, and 3 rearrangements 1110s Finished SNPs 1110s Finished ref gaps 1110s Finished read gaps 1110s Mutated reference genome to subject genome 1110s SNPs introduced: 3 1110s Reference gaps introduced: 0 1110s Read gaps introduced: 1 1110s Rearrangements introduced: 4 1110s Created read sampler 1110s Sampling 115 reads 1110s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1110s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1110s parsing sequence Sim.pm.1... 1110s parsing sequence Sim.pm.2... 1110s Parsed 7 reference bases 1110s *** Run 91 of 100 1110s /usr/bin/bowtie2 --np 14 --nofw --trim5 8 -i C,3.9295137622434 --score-min L,9.81090086648547,1.31551927692217 --cp-min 2 --mm --cp-ival 1 --trim3 6 --local -M 4 -q -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq 1111s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1111s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '1' because it was < 2 characters long 1111s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '5' because it was < 2 characters long 1111s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '6' because it was < 2 characters long 1111s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '7' because it was < 2 characters long 1111s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '8' because it was < 2 characters long 1111s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '9' because it was < 2 characters long 1111s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '11' because it was < 2 characters long 1111s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '12' because it was < 2 characters long 1111s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '13' because it was < 2 characters long 1111s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '14' because it was < 2 characters long 1111s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '16' because it was < 2 characters long 1111s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '22' because it was < 2 characters long 1111s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '25' because it was < 2 characters long 1111s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '29' because it was < 2 characters long 1111s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '30' because it was < 2 characters long 1111s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '32' because it was < 2 characters long 1111s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 1111s Warning: skipping read '33' because it was < 2 characters long 1111s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '34' because it was < 2 characters long 1111s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '36' because it was < 2 characters long 1111s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '41' because it was < 2 characters long 1111s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '44' because it was < 2 characters long 1111s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '46' because it was < 2 characters long 1111s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '47' because it was < 2 characters long 1111s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '51' because it was < 2 characters long 1111s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '52' because it was < 2 characters long 1111s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '59' because it was < 2 characters long 1111s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '60' because it was < 2 characters long 1111s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '62' because it was < 2 characters long 1111s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '64' because it was < 2 characters long 1111s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '65' because it was < 2 characters long 1111s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '66' because it was < 2 characters long 1111s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '67' because it was < 2 characters long 1111s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '68' because it was < 2 characters long 1111s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '69' because it was < 2 characters long 1111s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '70' because it was < 2 characters long 1111s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '71' because it was < 2 characters long 1111s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '72' because it was < 2 characters long 1111s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '74' because it was < 2 characters long 1111s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '77' because it was < 2 characters long 1111s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '78' because it was < 2 characters long 1111s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '81' because it was < 2 characters long 1111s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '82' because it was < 2 characters long 1111s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '83' because it was < 2 characters long 1111s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '84' because it was < 2 characters long 1111s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '85' because it was < 2 characters long 1111s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '88' because it was < 2 characters long 1111s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '89' because it was < 2 characters long 1111s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '94' because it was < 2 characters long 1111s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '97' because it was < 2 characters long 1111s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '98' because it was < 2 characters long 1111s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '99' because it was < 2 characters long 1111s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '103' because it was < 2 characters long 1111s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '104' because it was < 2 characters long 1111s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '105' because it was < 2 characters long 1111s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '106' because it was < 2 characters long 1111s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '107' because it was < 2 characters long 1111s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '109' because it was < 2 characters long 1111s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '110' because it was < 2 characters long 1111s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '113' because it was < 2 characters long 1111s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '114' because it was < 2 characters long 1111s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '115' because it was < 2 characters long 1111s 115 reads; of these: 1111s 115 (100.00%) were unpaired; of these: 1111s 115 (100.00%) aligned 0 times 1111s 0 (0.00%) aligned exactly 1 time 1111s 0 (0.00%) aligned >1 times 1111s 0.00% overall alignment rate 1111s Read 50 alignments... 1111s Read 100 alignments... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s --- Summary --- 1111s Read 1 reference strings 1111s Checked 0 alignments, 0 edits 1111s --------------- 1111s PASSED 1111s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1111s /usr/bin/bowtie2 --np 14 --nofw --trim5 8 -i C,3.9295137622434 --score-min L,9.81090086648547,1.31551927692217 --cp-min 2 --mm --cp-ival 1 --trim3 6 --local -M 4 -q -p 3 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1111s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1111s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '1' because it was < 2 characters long 1111s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '5' because it was < 2 characters long 1111s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '6' because it was < 2 characters long 1111s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '7' because it was < 2 characters long 1111s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '8' because it was < 2 characters long 1111s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '9' because it was < 2 characters long 1111s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '11' because it was < 2 characters long 1111s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '12' because it was < 2 characters long 1111s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '13' because it was < 2 characters long 1111s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '14' because it was < 2 characters long 1111s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '16' because it was < 2 characters long 1111s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '22' because it was < 2 characters long 1111s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '25' because it was < 2 characters long 1111s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '29' because it was < 2 characters long 1111s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '30' because it was < 2 characters long 1111s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '32' because it was < 2 characters long 1111s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 1111s Warning: skipping read '33' because it was < 2 characters long 1111s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '34' because it was < 2 characters long 1111s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '36' because it was < 2 characters long 1111s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '41' because it was < 2 characters long 1111s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '44' because it was < 2 characters long 1111s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '46' because it was < 2 characters long 1111s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '47' because it was < 2 characters long 1111s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '51' because it was < 2 characters long 1111s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '52' because it was < 2 characters long 1111s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '65' because it was < 2 characters long 1111s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '66' because it was < 2 characters long 1111s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '67' because it was < 2 characters long 1111s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '68' because it was < 2 characters long 1111s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '69' because it was < 2 characters long 1111s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '70' because it was < 2 characters long 1111s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '71' because it was < 2 characters long 1111s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '72' because it was < 2 characters long 1111s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '74' because it was < 2 characters long 1111s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '59' because it was < 2 characters long 1111s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '60' because it was < 2 characters long 1111s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '62' because it was < 2 characters long 1111s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '64' because it was < 2 characters long 1111s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '81' because it was < 2 characters long 1111s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '82' because it was < 2 characters long 1111s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '83' because it was < 2 characters long 1111s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '84' because it was < 2 characters long 1111s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '85' because it was < 2 characters long 1111s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '77' because it was < 2 characters long 1111s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '78' because it was < 2 characters long 1111s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '97' because it was < 2 characters long 1111s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '98' because it was < 2 characters long 1111s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '99' because it was < 2 characters long 1111s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '103' because it was < 2 characters long 1111s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '104' because it was < 2 characters long 1111s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '105' because it was < 2 characters long 1111s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '106' because it was < 2 characters long 1111s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '107' because it was < 2 characters long 1111s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '109' because it was < 2 characters long 1111s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '110' because it was < 2 characters long 1111s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '113' because it was < 2 characters long 1111s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '114' because it was < 2 characters long 1111s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '115' because it was < 2 characters long 1111s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '88' because it was < 2 characters long 1111s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '89' because it was < 2 characters long 1111s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '94' because it was < 2 characters long 1111s 115 reads; of these: 1111s 115 (100.00%) were unpaired; of these: 1111s 115 (100.00%) aligned 0 times 1111s 0 (0.00%) aligned exactly 1 time 1111s 0 (0.00%) aligned >1 times 1111s 0.00% overall alignment rate 1111s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1111s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1111s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1111s Flattened IUPAC characters 1111s Mutating sequence Sim.pm.2 1111s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1111s Finished SNPs 1111s Finished ref gaps 1111s Finished read gaps 1111s Mutating sequence Sim.pm.1 1111s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1111s Finished SNPs 1111s Finished ref gaps 1111s Finished read gaps 1111s Mutated reference genome to subject genome 1111s SNPs introduced: 3 1111s Reference gaps introduced: 0 1111s Read gaps introduced: 0 1111s Rearrangements introduced: 1 1111s Created read sampler 1111s Sampling 57 reads 1111s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1111s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1111s *** Run 92 of 100 1111s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 11 --trim3 6 -a -R 3 --nofw --np 2 --score-min L,6.97064901027138,6.16763820883317 --gbar 1 --trim5 3 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1111s parsing sequence Sim.pm.1... 1111s parsing sequence Sim.pm.2... 1111s Parsed 7 reference bases 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1111s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '3' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1111s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '6' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1111s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '9' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1111s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '15' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1111s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 1111s Warning: skipping read '18' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1111s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '20' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1111s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '21' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1111s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '25' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1111s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '32' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1111s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '33' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1111s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '36' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1111s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '39' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1111s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '43' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1111s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '44' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1111s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '47' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1111s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '49' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1111s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '53' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1111s 57 reads; of these: 1111s 57 (100.00%) were unpaired; of these: 1111s 56 (98.25%) aligned 0 times 1111s 1 (1.75%) aligned exactly 1 time 1111s 0 (0.00%) aligned >1 times 1111s 1.75% overall alignment rate 1111s Read 50 alignments... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s GAG 1111s GAG 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s Processing line... 1111s --- Summary --- 1111s Read 1 reference strings 1111s Checked 1 alignments, 0 edits 1111s --------------- 1111s PASSED 1111s ALSO checking that bowtie2 and bowtie2-align match up 1111s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 11 --trim3 6 -a -R 3 --nofw --np 2 --score-min L,6.97064901027138,6.16763820883317 --gbar 1 --trim5 3 -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1111s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '3' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1111s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '6' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1111s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '9' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1111s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '15' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1111s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 1111s Warning: skipping read '18' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1111s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '20' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1111s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '21' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1111s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '25' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1111s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '32' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1111s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '33' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1111s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '36' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1111s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '39' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1111s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '43' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1111s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '44' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1111s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '47' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1111s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '49' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1111s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1111s Warning: skipping read '53' because it was < 2 characters long 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1111s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1111s 57 reads; of these: 1111s 57 (100.00%) were unpaired; of these: 1111s 56 (98.25%) aligned 0 times 1111s 1 (1.75%) aligned exactly 1 time 1111s 0 (0.00%) aligned >1 times 1111s 1.75% overall alignment rate 1111s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1111s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1111s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 11 --trim3 6 -a -R 3 --nofw --np 2 --score-min L,6.97064901027138,6.16763820883317 --gbar 1 --trim5 3 -r -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.raw | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1112s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '3' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1112s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '6' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1112s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '9' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1112s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '15' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1112s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 1112s Warning: skipping read '18' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1112s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '20' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1112s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '21' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1112s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '25' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1112s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '32' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1112s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '33' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1112s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '36' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1112s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '39' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1112s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '49' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1112s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '53' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1112s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '43' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1112s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '44' because it was < 2 characters long 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1112s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1112s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1112s Warning: skipping read '47' because it was < 2 characters long 1112s 57 reads; of these: 1112s 57 (100.00%) were unpaired; of these: 1112s 56 (98.25%) aligned 0 times 1112s 1 (1.75%) aligned exactly 1 time 1112s 0 (0.00%) aligned >1 times 1112s 1.75% overall alignment rate 1112s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1112s Flattened IUPAC characters 1112s Mutating sequence Sim.pm.1 1112s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1112s Finished SNPs 1112s Finished ref gaps 1112s Finished read gaps 1112s Mutating sequence Sim.pm.2 1112s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1112s Finished SNPs 1112s Finished ref gaps 1112s Finished read gaps 1112s Mutated reference genome to subject genome 1112s SNPs introduced: 5 1112s Reference gaps introduced: 0 1112s Read gaps introduced: 0 1112s Rearrangements introduced: 1 1112s Created read sampler 1112s Sampling 126 reads 1112s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1112s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1112s parsing sequence Sim.pm.1... 1112s parsing sequence Sim.pm.2... 1112s Parsed 7 reference bases 1112s *** Run 93 of 100 1112s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mm --trim3 2 --rdg 2.19957682395542,2.47039775549612 --local -N 0 -R 3 --trim5 2 --rfg 33.3809015296291,17.0698271938298 --n-ceil 0.245862364721625,1.01930264948901 --score-min L,1.00093771288158,7.09740594275273 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1112s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '11' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1112s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 1112s Warning: skipping mate #2 of read '42' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1112s Read 50 alignments... 1112s Read 100 alignments... 1112s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '86' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '94' because length (1) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1112s Warning: skipping mate #2 of read '113' because length (1) <= # seed mismatches (0) 1112s Warning: skipping mate #2 of read '113' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '123' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '124' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '125' because it was < 2 characters long 1112s 126 reads; of these: 1112s 116 (92.06%) were paired; of these: 1112s 116 (100.00%) aligned concordantly 0 times 1112s 0 (0.00%) aligned concordantly exactly 1 time 1112s 0 (0.00%) aligned concordantly >1 times 1112s ---- 1112s 116 pairs aligned concordantly 0 times; of these: 1112s 0 (0.00%) aligned discordantly 1 time 1112s ---- 1112s 116 pairs aligned 0 times concordantly or discordantly; of these: 1112s 232 mates make up the pairs; of these: 1112s 232 (100.00%) aligned 0 times 1112s 0 (0.00%) aligned exactly 1 time 1112s 0 (0.00%) aligned >1 times 1112s 10 (7.94%) were unpaired; of these: 1112s 10 (100.00%) aligned 0 times 1112s 0 (0.00%) aligned exactly 1 time 1112s 0 (0.00%) aligned >1 times 1112s 0.00% overall alignment rate 1112s Read 150 alignments... 1112s Read 200 alignments... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s Processing line... 1112s --- Summary --- 1112s Read 1 reference strings 1112s Checked 0 alignments, 0 edits 1112s --------------- 1112s PASSED 1112s ALSO checking that bowtie2 and bowtie2-align match up 1112s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mm --trim3 2 --rdg 2.19957682395542,2.47039775549612 --local -N 0 -R 3 --trim5 2 --rfg 33.3809015296291,17.0698271938298 --n-ceil 0.245862364721625,1.01930264948901 --score-min L,1.00093771288158,7.09740594275273 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1112s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '11' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1112s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 1112s Warning: skipping mate #2 of read '42' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '86' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '94' because length (1) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1112s Warning: skipping mate #2 of read '113' because length (1) <= # seed mismatches (0) 1112s Warning: skipping mate #2 of read '113' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '123' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '124' because it was < 2 characters long 1112s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 1112s Warning: skipping mate #1 of read '125' because it was < 2 characters long 1112s 126 reads; of these: 1112s 116 (92.06%) were paired; of these: 1112s 116 (100.00%) aligned concordantly 0 times 1112s 0 (0.00%) aligned concordantly exactly 1 time 1112s 0 (0.00%) aligned concordantly >1 times 1112s ---- 1112s 116 pairs aligned concordantly 0 times; of these: 1112s 0 (0.00%) aligned discordantly 1 time 1112s ---- 1112s 116 pairs aligned 0 times concordantly or discordantly; of these: 1112s 232 mates make up the pairs; of these: 1112s 232 (100.00%) aligned 0 times 1112s 0 (0.00%) aligned exactly 1 time 1112s 0 (0.00%) aligned >1 times 1112s 10 (7.94%) were unpaired; of these: 1112s 10 (100.00%) aligned 0 times 1112s 0 (0.00%) aligned exactly 1 time 1112s 0 (0.00%) aligned >1 times 1112s 0.00% overall alignment rate 1112s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1112s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1112s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mm --trim3 2 --rdg 2.19957682395542,2.47039775549612 --local -N 0 -R 3 --trim5 2 --rfg 33.3809015296291,17.0698271938298 --n-ceil 0.245862364721625,1.01930264948901 --score-min L,1.00093771288158,7.09740594275273 -q -p 4 -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1112s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '11' because it was < 2 characters long 1113s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1113s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1113s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 1113s Warning: skipping mate #2 of read '42' because it was < 2 characters long 1113s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1113s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1113s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1113s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '86' because it was < 2 characters long 1113s Warning: skipping mate #2 of read '113' because length (1) <= # seed mismatches (0) 1113s Warning: skipping mate #2 of read '113' because it was < 2 characters long 1113s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '123' because it was < 2 characters long 1113s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '124' because it was < 2 characters long 1113s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '125' because it was < 2 characters long 1113s Warning: skipping mate #1 of read '94' because length (1) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1113s 126 reads; of these: 1113s 116 (92.06%) were paired; of these: 1113s 116 (100.00%) aligned concordantly 0 times 1113s 0 (0.00%) aligned concordantly exactly 1 time 1113s 0 (0.00%) aligned concordantly >1 times 1113s ---- 1113s 116 pairs aligned concordantly 0 times; of these: 1113s 0 (0.00%) aligned discordantly 1 time 1113s ---- 1113s 116 pairs aligned 0 times concordantly or discordantly; of these: 1113s 232 mates make up the pairs; of these: 1113s 232 (100.00%) aligned 0 times 1113s 0 (0.00%) aligned exactly 1 time 1113s 0 (0.00%) aligned >1 times 1113s 10 (7.94%) were unpaired; of these: 1113s 10 (100.00%) aligned 0 times 1113s 0 (0.00%) aligned exactly 1 time 1113s 0 (0.00%) aligned >1 times 1113s 0.00% overall alignment rate 1113s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1113s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1113s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1113s Flattened IUPAC characters 1113s Mutating sequence Sim.pm.1 1113s Introducing 3 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1113s Finished SNPs 1113s Finished ref gaps 1113s Finished read gaps 1113s Mutating sequence Sim.pm.2 1113s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1113s Finished SNPs 1113s Finished ref gaps 1113s Finished read gaps 1113s Mutated reference genome to subject genome 1113s SNPs introduced: 5 1113s Reference gaps introduced: 0 1113s Read gaps introduced: 2 1113s Rearrangements introduced: 0 1113s Created read sampler 1113s Sampling 100 reads 1113s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1113s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1113s parsing sequence Sim.pm.1... 1113s parsing sequence Sim.pm.2... 1113s Parsed 7 reference bases 1113s *** Run 94 of 100 1113s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 2 --norc --score-min L,4.73459870109376,4.64063749995743 --trim3 8 --mp 9.686037364096,5.95568937353492 -a -f -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fasta -2 /tmp/Sim.pm.dpFRpda2_2.fasta 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1113s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1113s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1113s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1113s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '21' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1113s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 1113s Warning: skipping mate #2 of read '25' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1113s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1113s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1113s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1113s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1113s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '49' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1113s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '50' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1113s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '54' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1113s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1113s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 1113s Warning: skipping mate #1 of read '92' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1113s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (0) 1113s Warning: skipping mate #2 of read '94' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1113s Read 50 alignments... 1113s Read 100 alignments... 1113s 100 reads; of these: 1113s 77 (77.00%) were paired; of these: 1113s 77 (100.00%) aligned concordantly 0 times 1113s 0 (0.00%) aligned concordantly exactly 1 time 1113s 0 (0.00%) aligned concordantly >1 times 1113s ---- 1113s 77 pairs aligned concordantly 0 times; of these: 1113s 0 (0.00%) aligned discordantly 1 time 1113s ---- 1113s 77 pairs aligned 0 times concordantly or discordantly; of these: 1113s 154 mates make up the pairs; of these: 1113s 153 (99.35%) aligned 0 times 1113s 1 (0.65%) aligned exactly 1 time 1113s 0 (0.00%) aligned >1 times 1113s 23 (23.00%) were unpaired; of these: 1113s 23 (100.00%) aligned 0 times 1113s 0 (0.00%) aligned exactly 1 time 1113s 0 (0.00%) aligned >1 times 1113s 0.56% overall alignment rate 1113s Read 150 alignments... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s GT 1113s GT 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s --- Summary --- 1113s Read 1 reference strings 1113s Checked 1 alignments, 0 edits 1113s --------------- 1113s PASSED 1113s Flattened IUPAC characters 1113s Mutating sequence Sim.pm.1 1113s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1113s Finished SNPs 1113s Finished ref gaps 1113s Finished read gaps 1113s Mutating sequence Sim.pm.2 1113s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1113s Finished SNPs 1113s Finished ref gaps 1113s Finished read gaps 1113s Mutated reference genome to subject genome 1113s SNPs introduced: 4 1113s Reference gaps introduced: 0 1113s Read gaps introduced: 0 1113s Rearrangements introduced: 0 1113s Created read sampler 1113s Sampling 85 reads 1113s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1113s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1113s parsing sequence Sim.pm.1... 1113s parsing sequence Sim.pm.2... 1113s Parsed 7 reference bases 1113s *** Run 95 of 100 1113s /usr/bin/bowtie2 --mm --cp-ival 4 --cp-min 5 --nofw --score-min L,3.27962585574398,1.37970654446401 --trim5 8 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1113s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '2' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1113s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '4' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1113s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '5' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1113s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '6' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1113s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '9' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1113s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '17' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1113s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '22' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1113s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '29' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1113s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '32' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1113s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '34' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1113s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 1113s Warning: skipping read '36' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1113s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '41' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1113s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '42' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1113s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '48' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1113s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '51' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1113s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '54' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1113s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 1113s Warning: skipping read '57' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1113s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '64' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1113s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '66' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1113s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '67' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1113s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '71' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1113s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '75' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1113s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '78' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1113s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '79' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1113s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1113s Warning: skipping read '84' because it was < 2 characters long 1113s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1113s 85 reads; of these: 1113s 85 (100.00%) were unpaired; of these: 1113s 83 (97.65%) aligned 0 times 1113s 2 (2.35%) aligned exactly 1 time 1113s 0 (0.00%) aligned >1 times 1113s 2.35% overall alignment rate 1113s Read 50 alignments... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s GTA 1113s GTA 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s GG 1113s GG 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s Processing line... 1113s --- Summary --- 1113s Read 1 reference strings 1113s Checked 2 alignments, 0 edits 1113s --------------- 1113s PASSED 1113s ALSO checking that bowtie2 and bowtie2-align match up 1113s /usr/bin/bowtie2 --mm --cp-ival 4 --cp-min 5 --nofw --score-min L,3.27962585574398,1.37970654446401 --trim5 8 -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1114s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '2' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1114s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '4' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1114s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '5' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1114s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '6' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1114s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '9' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1114s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '17' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1114s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '22' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1114s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '29' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1114s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '32' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1114s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '34' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1114s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '36' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1114s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '41' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1114s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '42' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1114s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '48' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1114s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '51' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1114s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '54' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1114s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '57' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1114s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '64' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1114s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '66' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1114s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '67' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1114s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '71' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1114s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '75' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1114s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '78' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1114s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '79' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1114s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1114s Warning: skipping read '84' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1114s 85 reads; of these: 1114s 85 (100.00%) were unpaired; of these: 1114s 83 (97.65%) aligned 0 times 1114s 2 (2.35%) aligned exactly 1 time 1114s 0 (0.00%) aligned >1 times 1114s 2.35% overall alignment rate 1114s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1114s Flattened IUPAC characters 1114s Mutating sequence Sim.pm.1 1114s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1114s Finished SNPs 1114s Finished ref gaps 1114s Finished read gaps 1114s *** Run 96 of 100 1114s /usr/bin/bowtie2 --nofw --cp-min 4 --cp-ival 2 -N 0 --rfg 7.5167678584928,7.13298272029661 -a --score-min L,7.42594444481902,3.91751824179154 --n-ceil 0.272015814027444,1.09919507146421 -q -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fastq 1114s Mutating sequence Sim.pm.2 1114s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1114s Finished SNPs 1114s Finished ref gaps 1114s Finished read gaps 1114s Mutated reference genome to subject genome 1114s SNPs introduced: 3 1114s Reference gaps introduced: 0 1114s Read gaps introduced: 0 1114s Rearrangements introduced: 1 1114s Created read sampler 1114s Sampling 143 reads 1114s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1114s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1114s parsing sequence Sim.pm.1... 1114s parsing sequence Sim.pm.2... 1114s Parsed 7 reference bases 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1114s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '58' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1114s Warning: skipping read '104' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '104' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1114s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '111' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1114s Warning: skipping read '131' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '131' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 1114s Warning: skipping read '136' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '136' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 1114s 143 reads; of these: 1114s 143 (100.00%) were unpaired; of these: 1114s 138 (96.50%) aligned 0 times 1114s 5 (3.50%) aligned exactly 1 time 1114s 0 (0.00%) aligned >1 times 1114s 3.50% overall alignment rate 1114s Read 50 alignments... 1114s Read 100 alignments... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s GAG 1114s GAG 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s GG 1114s GG 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s /usr/bin/bowtie2 --nofw --cp-min 4 --cp-ival 2 -N 0 --rfg 7.5167678584928,7.13298272029661 -a --score-min L,7.42594444481902,3.91751824179154 --n-ceil 0.272015814027444,1.09919507146421 -q -p 2 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s AGG 1114s AGG 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s GA 1114s GA 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s TA 1114s TA 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s Processing line... 1114s --- Summary --- 1114s Read 1 reference strings 1114s Checked 5 alignments, 0 edits 1114s --------------- 1114s PASSED 1114s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1114s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '58' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1114s Warning: skipping read '104' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '104' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1114s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '111' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1114s Warning: skipping read '131' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '131' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 1114s Warning: skipping read '136' because length (1) <= # seed mismatches (0) 1114s Warning: skipping read '136' because it was < 2 characters long 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1114s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1114s 143 reads; of these: 1114s 143 (100.00%) were unpaired; of these: 1114s 138 (96.50%) aligned 0 times 1114s 5 (3.50%) aligned exactly 1 time 1114s 0 (0.00%) aligned >1 times 1114s 3.50% overall alignment rate 1114s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1114s Flattened IUPAC characters 1114s Mutating sequence Sim.pm.2 1114s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1114s Finished SNPs 1114s Finished ref gaps 1114s Finished read gaps 1114s Mutating sequence Sim.pm.1 1114s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1114s Finished SNPs 1114s Finished ref gaps 1114s Finished read gaps 1114s Mutated reference genome to subject genome 1114s SNPs introduced: 5 1114s Reference gaps introduced: 1 1114s Read gaps introduced: 0 1114s Rearrangements introduced: 1 1114s Created read sampler 1114s Sampling 30 reads 1114s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.raw & /tmp/Sim.pm.dpFRpda2_2.raw 1114s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1114s parsing sequence Sim.pm.1... 1114s parsing sequence Sim.pm.2... 1114s Parsed 7 reference bases 1114s *** Run 97 of 100 1114s /usr/bin/bowtie2 --score-min L,7.84605696094914,8.85021814111087 --rdg 47.8327038738783,16.2424671396658 --local --cp-ival 1 --cp-min 7 --np 3 --nofw -r -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.raw 1115s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1115s *** Run 98 of 100 1115s /usr/bin/bowtie2 --cp-min 3 --cp-ival 2 --ma 5.77604522135288 --norc -N 0 -L20 --trim5 4 --score-min L,1.99043584670268,5.87495083891359 --gbar 2 --n-ceil 0.875463721069701,1.14527045439369 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq 1115s Warning: skipping read '22' because it was < 2 characters long 1115s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 1115s Warning: skipping read '25' because it was < 2 characters long 1115s 30 reads; of these: 1115s 30 (100.00%) were unpaired; of these: 1115s 30 (100.00%) aligned 0 times 1115s 0 (0.00%) aligned exactly 1 time 1115s 0 (0.00%) aligned >1 times 1115s 0.00% overall alignment rate 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s --- Summary --- 1115s Read 1 reference strings 1115s Checked 0 alignments, 0 edits 1115s --------------- 1115s PASSED 1115s Flattened IUPAC characters 1115s Mutating sequence Sim.pm.2 1115s Introducing 2 SNPs, 1/3 ref/read gaps, and 2 rearrangements 1115s Finished SNPs 1115s Finished ref gaps 1115s Finished read gaps 1115s Mutating sequence Sim.pm.1 1115s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1115s Finished SNPs 1115s Finished ref gaps 1115s Finished read gaps 1115s Mutated reference genome to subject genome 1115s SNPs introduced: 4 1115s Reference gaps introduced: 1 1115s Read gaps introduced: 3 1115s Rearrangements introduced: 2 1115s Created read sampler 1115s Sampling 51 reads 1115s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fastq & /tmp/Sim.pm.dpFRpda2_2.fastq 1115s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1115s parsing sequence Sim.pm.1... 1115s parsing sequence Sim.pm.2... 1115s Parsed 7 reference bases 1115s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1115s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1115s Warning: skipping read '3' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1115s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1115s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1115s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1115s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '22' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1115s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1115s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1115s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '29' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1115s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '33' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1115s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1115s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1115s Warning: skipping mate #2 of read '40' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1115s 51 reads; of these: 1115s 48 (94.12%) were paired; of these: 1115s 48 (100.00%) aligned concordantly 0 times 1115s 0 (0.00%) aligned concordantly exactly 1 time 1115s 0 (0.00%) aligned concordantly >1 times 1115s ---- 1115s 48 pairs aligned concordantly 0 times; of these: 1115s 0 (0.00%) aligned discordantly 1 time 1115s ---- 1115s 48 pairs aligned 0 times concordantly or discordantly; of these: 1115s 96 mates make up the pairs; of these: 1115s 96 (100.00%) aligned 0 times 1115s 0 (0.00%) aligned exactly 1 time 1115s 0 (0.00%) aligned >1 times 1115s 3 (5.88%) were unpaired; of these: 1115s 3 (100.00%) aligned 0 times 1115s 0 (0.00%) aligned exactly 1 time 1115s 0 (0.00%) aligned >1 times 1115s 0.00% overall alignment rate 1115s Read 50 alignments... 1115s Read 100 alignments... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s Processing line... 1115s --- Summary --- 1115s Read 1 reference strings 1115s Checked 0 alignments, 0 edits 1115s --------------- 1115s PASSED 1115s ALSO checking that bowtie2 and bowtie2-align match up 1115s /usr/bin/bowtie2 --cp-min 3 --cp-ival 2 --ma 5.77604522135288 --norc -N 0 -L20 --trim5 4 --score-min L,1.99043584670268,5.87495083891359 --gbar 2 --n-ceil 0.875463721069701,1.14527045439369 -q -x /tmp/Sim.pm.dpFRpda2 -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1115s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1115s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1115s Warning: skipping read '3' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1115s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1115s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1115s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1115s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '22' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1115s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1115s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1115s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '29' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1115s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '33' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1115s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1115s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1115s Warning: skipping mate #2 of read '40' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1115s 51 reads; of these: 1115s 48 (94.12%) were paired; of these: 1115s 48 (100.00%) aligned concordantly 0 times 1115s 0 (0.00%) aligned concordantly exactly 1 time 1115s 0 (0.00%) aligned concordantly >1 times 1115s ---- 1115s 48 pairs aligned concordantly 0 times; of these: 1115s 0 (0.00%) aligned discordantly 1 time 1115s ---- 1115s 48 pairs aligned 0 times concordantly or discordantly; of these: 1115s 96 mates make up the pairs; of these: 1115s 96 (100.00%) aligned 0 times 1115s 0 (0.00%) aligned exactly 1 time 1115s 0 (0.00%) aligned >1 times 1115s 3 (5.88%) were unpaired; of these: 1115s 3 (100.00%) aligned 0 times 1115s 0 (0.00%) aligned exactly 1 time 1115s 0 (0.00%) aligned >1 times 1115s 0.00% overall alignment rate 1115s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1115s /usr/bin/bowtie2 --cp-min 3 --cp-ival 2 --ma 5.77604522135288 --norc -N 0 -L20 --trim5 4 --score-min L,1.99043584670268,5.87495083891359 --gbar 2 --n-ceil 0.875463721069701,1.14527045439369 -q -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder -1 /tmp/Sim.pm.dpFRpda2_1.fastq -2 /tmp/Sim.pm.dpFRpda2_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1115s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1115s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1115s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1115s Warning: skipping read '3' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1115s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1115s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1115s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '22' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1115s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1115s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1115s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '33' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1115s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1115s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1115s Warning: skipping mate #2 of read '40' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1115s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1115s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1115s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 1115s Warning: skipping mate #2 of read '29' because it was < 2 characters long 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1115s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1115s 51 reads; of these: 1115s 48 (94.12%) were paired; of these: 1115s 48 (100.00%) aligned concordantly 0 times 1115s 0 (0.00%) aligned concordantly exactly 1 time 1115s 0 (0.00%) aligned concordantly >1 times 1115s ---- 1115s 48 pairs aligned concordantly 0 times; of these: 1115s 0 (0.00%) aligned discordantly 1 time 1115s ---- 1115s 48 pairs aligned 0 times concordantly or discordantly; of these: 1115s 96 mates make up the pairs; of these: 1115s 96 (100.00%) aligned 0 times 1115s 0 (0.00%) aligned exactly 1 time 1115s 0 (0.00%) aligned >1 times 1115s 3 (5.88%) were unpaired; of these: 1115s 3 (100.00%) aligned 0 times 1115s 0 (0.00%) aligned exactly 1 time 1115s 0 (0.00%) aligned >1 times 1115s 0.00% overall alignment rate 1115s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1115s Flattened IUPAC characters 1115s Mutating sequence Sim.pm.1 1115s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1115s Finished SNPs 1115s Finished ref gaps 1115s Finished read gaps 1115s Mutating sequence Sim.pm.2 1115s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1115s Finished SNPs 1115s Finished ref gaps 1115s Finished read gaps 1115s Mutated reference genome to subject genome 1115s SNPs introduced: 7 1115s Reference gaps introduced: 0 1115s Read gaps introduced: 0 1115s Rearrangements introduced: 0 1115s Created read sampler 1115s Sampling 42 reads 1115s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1115s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1115s parsing sequence Sim.pm.1... 1115s parsing sequence Sim.pm.2... 1115s Parsed 7 reference bases 1115s *** Run 99 of 100 1115s /usr/bin/bowtie2 --cp-ival 1 --cp-min 2 --n-ceil 0.187439425118431,1.21245592881867 --score-min L,3.96290501712213,7.00252297949719 --trim5 1 --trim3 9 --local -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1116s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '3' because it was < 2 characters long 1116s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '5' because it was < 2 characters long 1116s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '7' because it was < 2 characters long 1116s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '10' because it was < 2 characters long 1116s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '11' because it was < 2 characters long 1116s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '13' because it was < 2 characters long 1116s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '14' because it was < 2 characters long 1116s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '22' because it was < 2 characters long 1116s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '26' because it was < 2 characters long 1116s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '29' because it was < 2 characters long 1116s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '30' because it was < 2 characters long 1116s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '31' because it was < 2 characters long 1116s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '32' because it was < 2 characters long 1116s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '34' because it was < 2 characters long 1116s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '36' because it was < 2 characters long 1116s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '38' because it was < 2 characters long 1116s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '40' because it was < 2 characters long 1116s 42 reads; of these: 1116s 42 (100.00%) were unpaired; of these: 1116s 42 (100.00%) aligned 0 times 1116s 0 (0.00%) aligned exactly 1 time 1116s 0 (0.00%) aligned >1 times 1116s 0.00% overall alignment rate 1116s Processing line... 1116s /usr/bin/bowtie2 --cp-ival 1 --cp-min 2 --n-ceil 0.187439425118431,1.21245592881867 --score-min L,3.96290501712213,7.00252297949719 --trim5 1 --trim3 9 --local -f -p 4 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s --- Summary --- 1116s Read 1 reference strings 1116s Checked 0 alignments, 0 edits 1116s --------------- 1116s PASSED 1116s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1116s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '3' because it was < 2 characters long 1116s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '5' because it was < 2 characters long 1116s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '7' because it was < 2 characters long 1116s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '10' because it was < 2 characters long 1116s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '11' because it was < 2 characters long 1116s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '13' because it was < 2 characters long 1116s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '14' because it was < 2 characters long 1116s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '22' because it was < 2 characters long 1116s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '26' because it was < 2 characters long 1116s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '29' because it was < 2 characters long 1116s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '30' because it was < 2 characters long 1116s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '31' because it was < 2 characters long 1116s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '32' because it was < 2 characters long 1116s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '34' because it was < 2 characters long 1116s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '36' because it was < 2 characters long 1116s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '38' because it was < 2 characters long 1116s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '40' because it was < 2 characters long 1116s 42 reads; of these: 1116s 42 (100.00%) were unpaired; of these: 1116s 42 (100.00%) aligned 0 times 1116s 0 (0.00%) aligned exactly 1 time 1116s 0 (0.00%) aligned >1 times 1116s 0.00% overall alignment rate 1116s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1116s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1116s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1116s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1116s /usr/bin/bowtie2 --cp-ival 1 --cp-min 2 --n-ceil 0.187439425118431,1.21245592881867 --score-min L,3.96290501712213,7.00252297949719 --trim5 1 --trim3 9 --local -f -p 3 -x /tmp/Sim.pm.dpFRpda2 --reorder /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.reord.als 1116s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '3' because it was < 2 characters long 1116s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '5' because it was < 2 characters long 1116s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '7' because it was < 2 characters long 1116s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '10' because it was < 2 characters long 1116s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '11' because it was < 2 characters long 1116s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '13' because it was < 2 characters long 1116s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '14' because it was < 2 characters long 1116s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '22' because it was < 2 characters long 1116s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '26' because it was < 2 characters long 1116s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '29' because it was < 2 characters long 1116s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1116s Warning: skipping read '30' because it was < 2 characters long 1116s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '31' because it was < 2 characters long 1116s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '32' because it was < 2 characters long 1116s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '34' because it was < 2 characters long 1116s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '36' because it was < 2 characters long 1116s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '38' because it was < 2 characters long 1116s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '40' because it was < 2 characters long 1116s 42 reads; of these: 1116s 42 (100.00%) were unpaired; of these: 1116s 42 (100.00%) aligned 0 times 1116s 0 (0.00%) aligned exactly 1 time 1116s 0 (0.00%) aligned >1 times 1116s 0.00% overall alignment rate 1116s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als /tmp/Sim.pm.dpFRpda2.px.reord.als 1116s Flattened IUPAC characters 1116s Mutating sequence Sim.pm.2 1116s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1116s Finished SNPs 1116s Finished ref gaps 1116s Finished read gaps 1116s Mutating sequence Sim.pm.1 1116s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1116s Finished SNPs 1116s Finished ref gaps 1116s Finished read gaps 1116s Mutated reference genome to subject genome 1116s SNPs introduced: 4 1116s Reference gaps introduced: 0 1116s Read gaps introduced: 0 1116s Rearrangements introduced: 1 1116s Created read sampler 1116s Sampling 33 reads 1116s Dumping reads to temporary files /tmp/Sim.pm.dpFRpda2_1.fasta & /tmp/Sim.pm.dpFRpda2_2.fasta 1116s Parsing FASTA file /tmp/Sim.pm.dpFRpda2.fa... 1116s parsing sequence Sim.pm.1... 1116s parsing sequence Sim.pm.2... 1116s Parsed 7 reference bases 1116s *** Run 100 of 100 1116s /usr/bin/bowtie2 --np 1 --nofw --score-min L,2.15304753650401,6.24336840523701 --mm --cp-ival 1 --cp-min 2 -M 6 --rdg 19.0238234703545,19.3339748389031 --trim3 3 --local -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta 1116s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1116s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '6' because it was < 2 characters long 1116s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '12' because it was < 2 characters long 1116s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '26' because it was < 2 characters long 1116s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1116s Warning: skipping read '30' because it was < 2 characters long 1116s 33 reads; of these: 1116s 33 (100.00%) were unpaired; of these: 1116s 33 (100.00%) aligned 0 times 1116s 0 (0.00%) aligned exactly 1 time 1116s 0 (0.00%) aligned >1 times 1116s 0.00% overall alignment rate 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s Processing line... 1116s --- Summary --- 1116s Read 1 reference strings 1116s Checked 0 alignments, 0 edits 1116s --------------- 1116s PASSED 1116s ALSO checking that bowtie2 and bowtie2-align match up 1116s /usr/bin/bowtie2 --np 1 --nofw --score-min L,2.15304753650401,6.24336840523701 --mm --cp-ival 1 --cp-min 2 -M 6 --rdg 19.0238234703545,19.3339748389031 --trim3 3 --local -f -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.als 1117s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1117s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1117s Warning: skipping read '6' because it was < 2 characters long 1117s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1117s Warning: skipping read '12' because it was < 2 characters long 1117s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1117s Warning: skipping read '26' because it was < 2 characters long 1117s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1117s Warning: skipping read '30' because it was < 2 characters long 1117s 33 reads; of these: 1117s 33 (100.00%) were unpaired; of these: 1117s 33 (100.00%) aligned 0 times 1117s 0 (0.00%) aligned exactly 1 time 1117s 0 (0.00%) aligned >1 times 1117s 0.00% overall alignment rate 1117s diff -uw /tmp/Sim.pm.dpFRpda2.als /tmp/Sim.pm.dpFRpda2.debug.als 1117s /usr/bin/bowtie2 --np 1 --nofw --score-min L,2.15304753650401,6.24336840523701 --mm --cp-ival 1 --cp-min 2 -M 6 --rdg 19.0238234703545,19.3339748389031 --trim3 3 --local -f -p 4 -x /tmp/Sim.pm.dpFRpda2 /tmp/Sim.pm.dpFRpda2_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als 1117s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1117s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1117s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1117s Warning: skipping read '6' because it was < 2 characters long 1117s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1117s Warning: skipping read '12' because it was < 2 characters long 1117s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1117s Warning: skipping read '26' because it was < 2 characters long 1117s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1117s Warning: skipping read '30' because it was < 2 characters long 1117s 33 reads; of these: 1117s 33 (100.00%) were unpaired; of these: 1117s 33 (100.00%) aligned 0 times 1117s 0 (0.00%) aligned exactly 1 time 1117s 0 (0.00%) aligned >1 times 1117s 0.00% overall alignment rate 1117s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.px.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.px.als.sorted 1117s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.dpFRpda2.debug.als | grep -v '^@PG' > /tmp/Sim.pm.dpFRpda2.debug.als.sorted 1117s diff -uw /tmp/Sim.pm.dpFRpda2.debug.als.sorted /tmp/Sim.pm.dpFRpda2.px.als.sorted 1117s Created DNA generator 1117s N frac: 0.035 1117s IUPAC frac: 0.002 1117s AT/ACGT frac: 0.428 1117s A/AT frac: 0.629 1117s C/CG frac: 0.345 1117s Generating 2 references 1117s Generated reference 'Sim.pm.1' of untrimmed length 122, trimmed length 31 1117s Generated reference 'Sim.pm.2' of untrimmed length 329, trimmed length 238 1117s Wrote references to /tmp/Sim.pm.4OZZSEW9.fa 1117s A: 75 1117s C: 60 1117s G: 82 1117s N: 10 1117s T: 42 1117s *** TEST CASE *** 1117s Executing: /usr/bin/bowtie2-build --large-index --dcv 128 --threads 1 /tmp/Sim.pm.4OZZSEW9.fa /tmp/Sim.pm.4OZZSEW9 1117s Settings: 1117s Output files: "/tmp/Sim.pm.4OZZSEW9.*.bt2l" 1117s Line rate: 7 (line is 128 bytes) 1117s Lines per side: 1 (side is 128 bytes) 1117s Offset rate: 4 (one in 16) 1117s FTable chars: 10 1117s Strings: unpacked 1117s Max bucket size: default 1117s Max bucket size, sqrt multiplier: default 1117s Max bucket size, len divisor: 4 1117s Difference-cover sample period: 128 1117s Endianness: little 1117s Actual local endianness: little 1117s Sanity checking: disabled 1117s Assertions: disabled 1117s Random seed: 0 1117s Sizeofs: void*:8, int:4, long:8, size_t:8 1117s Input files DNA, FASTA: 1117s /tmp/Sim.pm.4OZZSEW9.fa 1117s Building a LARGE index 1117s Reading reference sizes 1117s Time reading reference sizes: 00:00:00 1117s Calculating joined length 1117s Writing header 1117s Reserving space for joined string 1117s Joining reference sequences 1117s Time to join reference sequences: 00:00:00 1117s bmax according to bmaxDivN setting: 64 1117s Using parameters --bmax 48 --dcv 128 1117s Doing ahead-of-time memory usage test 1117s Passed! Constructing with these parameters: --bmax 48 --dcv 128 1117s Constructing suffix-array element generator 1117s Building DifferenceCoverSample 1117s Building sPrime 1117s Building sPrimeOrder 1117s V-Sorting samples 1117s V-Sorting samples time: 00:00:00 1117s Allocating rank array 1117s Ranking v-sort output 1117s Ranking v-sort output time: 00:00:00 1117s Invoking Larsson-Sadakane on ranks 1117s Invoking Larsson-Sadakane on ranks time: 00:00:00 1117s Sanity-checking and returning 1117s Building samples 1117s Reserving space for 12 sample suffixes 1117s Generating random suffixes 1117s QSorting 12 sample offsets, eliminating duplicates 1117s QSorting sample offsets, eliminating duplicates time: 00:00:00 1117s Multikey QSorting 12 samples 1117s (Using difference cover) 1117s Multikey QSorting samples time: 00:00:00 1117s Calculating bucket sizes 1117s Splitting and merging 1117s Splitting and merging time: 00:00:00 1117s Avg bucket size: 31.5 (target: 47) 1117s Converting suffix-array elements to index image 1117s Allocating ftab, absorbFtab 1117s Entering Ebwt loop 1117s Getting block 1 of 8 1117s Reserving size (48) for bucket 1 1117s Calculating Z arrays for bucket 1 1117s Entering block accumulator loop for bucket 1: 1117s bucket 1: 10% 1117s bucket 1: 20% 1117s bucket 1: 30% 1117s bucket 1: 40% 1117s bucket 1: 50% 1117s bucket 1: 60% 1117s bucket 1: 70% 1117s bucket 1: 80% 1117s bucket 1: 90% 1117s bucket 1: 100% 1117s Sorting block of length 11 for bucket 1 1117s (Using difference cover) 1117s Sorting block time: 00:00:00 1117s Returning block of 12 for bucket 1 1117s Getting block 2 of 8 1117s Reserving size (48) for bucket 2 1117s Calculating Z arrays for bucket 2 1117s Entering block accumulator loop for bucket 2: 1117s bucket 2: 10% 1117s bucket 2: 20% 1117s bucket 2: 30% 1117s bucket 2: 40% 1117s bucket 2: 50% 1117s bucket 2: 60% 1117s bucket 2: 70% 1117s bucket 2: 80% 1117s bucket 2: 90% 1117s bucket 2: 100% 1117s Sorting block of length 46 for bucket 2 1117s (Using difference cover) 1117s Sorting block time: 00:00:00 1117s Returning block of 47 for bucket 2 1117s Getting block 3 of 8 1117s Reserving size (48) for bucket 3 1117s Calculating Z arrays for bucket 3 1117s Entering block accumulator loop for bucket 3: 1117s bucket 3: 10% 1117s bucket 3: 20% 1117s bucket 3: 30% 1117s bucket 3: 40% 1117s bucket 3: 50% 1117s bucket 3: 60% 1117s bucket 3: 70% 1117s bucket 3: 80% 1117s bucket 3: 90% 1117s bucket 3: 100% 1117s Sorting block of length 18 for bucket 3 1117s (Using difference cover) 1117s Sorting block time: 00:00:00 1117s Returning block of 19 for bucket 3 1117s Getting block 4 of 8 1117s Reserving size (48) for bucket 4 1117s Calculating Z arrays for bucket 4 1117s Entering block accumulator loop for bucket 4: 1117s bucket 4: 10% 1117s bucket 4: 20% 1117s bucket 4: 30% 1117s bucket 4: 40% 1117s bucket 4: 50% 1117s bucket 4: 60% 1117s bucket 4: 70% 1117s bucket 4: 80% 1117s bucket 4: 90% 1117s bucket 4: 100% 1117s Sorting block of length 29 for bucket 4 1117s (Using difference cover) 1117s Sorting block time: 00:00:00 1117s Returning block of 30 for bucket 4 1117s Getting block 5 of 8 1117s Reserving size (48) for bucket 5 1117s Calculating Z arrays for bucket 5 1117s Entering block accumulator loop for bucket 5: 1117s bucket 5: 10% 1117s bucket 5: 20% 1117s bucket 5: 30% 1117s bucket 5: 40% 1117s bucket 5: 50% 1117s bucket 5: 60% 1117s bucket 5: 70% 1117s bucket 5: 80% 1117s bucket 5: 90% 1117s bucket 5: 100% 1117s Sorting block of length 42 for bucket 5 1117s (Using difference cover) 1117s Sorting block time: 00:00:00 1117s Returning block of 43 for bucket 5 1117s Getting block 6 of 8 1117s Reserving size (48) for bucket 6 1117s Calculating Z arrays for bucket 6 1117s Entering block accumulator loop for bucket 6: 1117s bucket 6: 10% 1117s bucket 6: 20% 1117s bucket 6: 30% 1117s bucket 6: 40% 1117s bucket 6: 50% 1117s bucket 6: 60% 1117s bucket 6: 70% 1117s bucket 6: 80% 1117s bucket 6: 90% 1117s bucket 6: 100% 1117s Sorting block of length 45 for bucket 6 1117s (Using difference cover) 1117s Sorting block time: 00:00:00 1117s Returning block of 46 for bucket 6 1117s Getting block 7 of 8 1117s Reserving size (48) for bucket 7 1117s Calculating Z arrays for bucket 7 1117s Entering block accumulator loop for bucket 7: 1117s bucket 7: 10% 1117s bucket 7: 20% 1117s bucket 7: 30% 1117s bucket 7: 40% 1117s bucket 7: 50% 1117s bucket 7: 60% 1117s bucket 7: 70% 1117s bucket 7: 80% 1117s bucket 7: 90% 1117s bucket 7: 100% 1117s Sorting block of length 42 for bucket 7 1117s (Using difference cover) 1117s Sorting block time: 00:00:00 1117s Returning block of 43 for bucket 7 1117s Getting block 8 of 8 1117s Reserving size (48) for bucket 8 1117s Calculating Z arrays for bucket 8 1117s Entering block accumulator loop for bucket 8: 1117s bucket 8: 10% 1117s bucket 8: 20% 1117s bucket 8: 30% 1117s bucket 8: 40% 1117s bucket 8: 50% 1117s bucket 8: 60% 1117s bucket 8: 70% 1117s bucket 8: 80% 1117s bucket 8: 90% 1117s bucket 8: 100% 1117s Sorting block of length 19 for bucket 8 1117s (Using difference cover) 1117s Sorting block time: 00:00:00 1117s Returning block of 20 for bucket 8 1117s Exited Ebwt loop 1117s fchr[A]: 0 1117s fchr[C]: 75 1117s fchr[G]: 135 1117s fchr[T]: 217 1117s fchr[$]: 259 1118s Exiting Ebwt::buildToDisk() 1118s Returning from initFromVector 1118s Wrote 8389323 bytes to primary EBWT file: /tmp/Sim.pm.4OZZSEW9.1.bt2l.tmp 1118s Wrote 140 bytes to secondary EBWT file: /tmp/Sim.pm.4OZZSEW9.2.bt2l.tmp 1118s Re-opening _in1 and _in2 as input streams 1118s Returning from Ebwt constructor 1118s Headers: 1118s len: 259 1118s bwtLen: 260 1118s sz: 65 1118s bwtSz: 65 1118s lineRate: 7 1118s offRate: 4 1118s offMask: 0xfffffffffffffff0 1118s ftabChars: 10 1118s eftabLen: 20 1118s eftabSz: 160 1118s ftabLen: 1048577 1118s ftabSz: 8388616 1118s offsLen: 17 1118s offsSz: 136 1118s lineSz: 128 1118s sideSz: 128 1118s sideBwtSz: 96 1118s sideBwtLen: 384 1118s numSides: 1 1118s numLines: 1 1118s ebwtTotLen: 128 1118s ebwtTotSz: 128 1118s color: 0 1118s reverse: 0 1118s Total time for call to driver() for forward index: 00:00:00 1118s Reading reference sizes 1118s Time reading reference sizes: 00:00:00 1118s Calculating joined length 1118s Writing header 1118s Reserving space for joined string 1118s Joining reference sequences 1118s Time to join reference sequences: 00:00:00 1118s Time to reverse reference sequence: 00:00:00 1118s bmax according to bmaxDivN setting: 64 1118s Using parameters --bmax 48 --dcv 128 1118s Doing ahead-of-time memory usage test 1118s Passed! Constructing with these parameters: --bmax 48 --dcv 128 1118s Constructing suffix-array element generator 1118s Building DifferenceCoverSample 1118s Building sPrime 1118s Building sPrimeOrder 1118s V-Sorting samples 1118s V-Sorting samples time: 00:00:00 1118s Allocating rank array 1118s Ranking v-sort output 1118s Ranking v-sort output time: 00:00:00 1118s Invoking Larsson-Sadakane on ranks 1118s Invoking Larsson-Sadakane on ranks time: 00:00:00 1118s Sanity-checking and returning 1118s Building samples 1118s Reserving space for 12 sample suffixes 1118s Generating random suffixes 1118s QSorting 12 sample offsets, eliminating duplicates 1118s QSorting sample offsets, eliminating duplicates time: 00:00:00 1118s Multikey QSorting 12 samples 1118s (Using difference cover) 1118s Multikey QSorting samples time: 00:00:00 1118s Calculating bucket sizes 1118s Splitting and merging 1118s Splitting and merging time: 00:00:00 1118s Avg bucket size: 36.1429 (target: 47) 1118s Converting suffix-array elements to index image 1118s Allocating ftab, absorbFtab 1118s Entering Ebwt loop 1118s Getting block 1 of 7 1118s Reserving size (48) for bucket 1 1118s Calculating Z arrays for bucket 1 1118s Entering block accumulator loop for bucket 1: 1118s bucket 1: 10% 1118s bucket 1: 20% 1118s bucket 1: 30% 1118s bucket 1: 40% 1118s bucket 1: 50% 1118s bucket 1: 60% 1118s bucket 1: 70% 1118s bucket 1: 80% 1118s bucket 1: 90% 1118s bucket 1: 100% 1118s Sorting block of length 19 for bucket 1 1118s (Using difference cover) 1118s Sorting block time: 00:00:00 1118s Returning block of 20 for bucket 1 1118s Getting block 2 of 7 1118s Reserving size (48) for bucket 2 1118s Calculating Z arrays for bucket 2 1118s Entering block accumulator loop for bucket 2: 1118s bucket 2: 10% 1118s bucket 2: 20% 1118s bucket 2: 30% 1118s bucket 2: 40% 1118s bucket 2: 50% 1118s bucket 2: 60% 1118s bucket 2: 70% 1118s bucket 2: 80% 1118s bucket 2: 90% 1118s bucket 2: 100% 1118s Sorting block of length 40 for bucket 2 1118s (Using difference cover) 1118s Sorting block time: 00:00:00 1118s Returning block of 41 for bucket 2 1118s Getting block 3 of 7 1118s Reserving size (48) for bucket 3 1118s Calculating Z arrays for bucket 3 1118s Entering block accumulator loop for bucket 3: 1118s bucket 3: 10% 1118s bucket 3: 20% 1118s bucket 3: 30% 1118s bucket 3: 40% 1118s bucket 3: 50% 1118s bucket 3: 60% 1118s bucket 3: 70% 1118s bucket 3: 80% 1118s bucket 3: 90% 1118s bucket 3: 100% 1118s Sorting block of length 30 for bucket 3 1118s (Using difference cover) 1118s Sorting block time: 00:00:00 1118s Returning block of 31 for bucket 3 1118s Getting block 4 of 7 1118s Reserving size (48) for bucket 4 1118s Calculating Z arrays for bucket 4 1118s Entering block accumulator loop for bucket 4: 1118s bucket 4: 10% 1118s bucket 4: 20% 1118s bucket 4: 30% 1118s bucket 4: 40% 1118s bucket 4: 50% 1118s bucket 4: 60% 1118s bucket 4: 70% 1118s bucket 4: 80% 1118s bucket 4: 90% 1118s bucket 4: 100% 1118s Sorting block of length 43 for bucket 4 1118s (Using difference cover) 1118s Sorting block time: 00:00:00 1118s Returning block of 44 for bucket 4 1118s Getting block 5 of 7 1118s Reserving size (48) for bucket 5 1118s Calculating Z arrays for bucket 5 1118s Entering block accumulator loop for bucket 5: 1118s bucket 5: 10% 1118s bucket 5: 20% 1118s bucket 5: 30% 1118s bucket 5: 40% 1118s bucket 5: 50% 1118s bucket 5: 60% 1118s bucket 5: 70% 1118s bucket 5: 80% 1118s bucket 5: 90% 1118s bucket 5: 100% 1118s Sorting block of length 47 for bucket 5 1118s (Using difference cover) 1118s Sorting block time: 00:00:00 1118s Returning block of 48 for bucket 5 1118s Getting block 6 of 7 1118s Reserving size (48) for bucket 6 1118s Calculating Z arrays for bucket 6 1118s Entering block accumulator loop for bucket 6: 1118s bucket 6: 10% 1118s bucket 6: 20% 1118s bucket 6: 30% 1118s bucket 6: 40% 1118s bucket 6: 50% 1118s bucket 6: 60% 1118s bucket 6: 70% 1118s bucket 6: 80% 1118s bucket 6: 90% 1118s bucket 6: 100% 1118s Sorting block of length 42 for bucket 6 1118s (Using difference cover) 1118s Sorting block time: 00:00:00 1118s Returning block of 43 for bucket 6 1118s Getting block 7 of 7 1118s Reserving size (48) for bucket 7 1118s Calculating Z arrays for bucket 7 1118s Entering block accumulator loop for bucket 7: 1118s bucket 7: 10% 1118s bucket 7: 20% 1118s bucket 7: 30% 1118s bucket 7: 40% 1118s bucket 7: 50% 1118s bucket 7: 60% 1118s bucket 7: 70% 1118s bucket 7: 80% 1118s bucket 7: 90% 1118s bucket 7: 100% 1118s Sorting block of length 32 for bucket 7 1118s (Using difference cover) 1118s Sorting block time: 00:00:00 1118s Returning block of 33 for bucket 7 1118s Exited Ebwt loop 1118s fchr[A]: 0 1118s fchr[C]: 75 1118s fchr[G]: 135 1118s fchr[T]: 217 1118s fchr[$]: 259 1118s Exiting Ebwt::buildToDisk() 1118s Returning from initFromVector 1118s Wrote 8389323 bytes to primary EBWT file: /tmp/Sim.pm.4OZZSEW9.rev.1.bt2l.tmp 1118s Wrote 140 bytes to secondary EBWT file: /tmp/Sim.pm.4OZZSEW9.rev.2.bt2l.tmp 1118s Re-opening _in1 and _in2 as input streams 1118s Renaming /tmp/Sim.pm.4OZZSEW9.3.bt2l.tmp to /tmp/Sim.pm.4OZZSEW9.3.bt2l 1118s Returning from Ebwt constructor 1118s Headers: 1118s len: 259 1118s bwtLen: 260 1118s sz: 65 1118s bwtSz: 65 1118s lineRate: 7 1118s offRate: 4 1118s offMask: 0xfffffffffffffff0 1118s ftabChars: 10 1118s eftabLen: 20 1118s eftabSz: 160 1118s ftabLen: 1048577 1118s ftabSz: 8388616 1118s offsLen: 17 1118s offsSz: 136 1118s lineSz: 128 1118s sideSz: 128 1118s sideBwtSz: 96 1118s sideBwtLen: 384 1118s numSides: 1 1118s numLines: 1 1118s ebwtTotLen: 128 1118s ebwtTotSz: 128 1118s color: 0 1118s reverse: 1 1118s Total time for backward call to driver() for mirror index: 00:00:01 1118s Renaming /tmp/Sim.pm.4OZZSEW9.4.bt2l.tmp to /tmp/Sim.pm.4OZZSEW9.4.bt2l 1118s Renaming /tmp/Sim.pm.4OZZSEW9.1.bt2l.tmp to /tmp/Sim.pm.4OZZSEW9.1.bt2l 1118s Renaming /tmp/Sim.pm.4OZZSEW9.2.bt2l.tmp to /tmp/Sim.pm.4OZZSEW9.2.bt2l 1118s Renaming /tmp/Sim.pm.4OZZSEW9.rev.1.bt2l.tmp to /tmp/Sim.pm.4OZZSEW9.rev.1.bt2l 1118s Renaming /tmp/Sim.pm.4OZZSEW9.rev.2.bt2l.tmp to /tmp/Sim.pm.4OZZSEW9.rev.2.bt2l 1118s Built nucleotide index '/tmp/Sim.pm.4OZZSEW9' 1118s Flattened IUPAC characters 1118s Mutating sequence Sim.pm.1 1118s Introducing 5 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1118s Finished SNPs 1118s Finished ref gaps 1118s Finished read gaps 1118s Mutating sequence Sim.pm.2 1118s Introducing 21 SNPs, 2/0 ref/read gaps, and 1 rearrangements 1118s Finished SNPs 1118s Finished ref gaps 1118s Finished read gaps 1118s Mutated reference genome to subject genome 1118s SNPs introduced: 26 1118s Reference gaps introduced: 2 1118s Read gaps introduced: 2 1118s Rearrangements introduced: 1 1118s Created read sampler 1118s Sampling 143 reads 1118s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1118s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1118s parsing sequence Sim.pm.1... 1118s parsing sequence Sim.pm.2... 1118s Parsed 269 reference bases 1118s *** Run 1 of 100 1118s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --ma 2.79945143542875 --large-index -k 9 --rdg 11.4573630289528 -N 0 -L22 -R 2 -D 47 --nofw --np 4 --n-ceil 1.1628031131524,0.914145545662554 --score-min L,3.21375200672491,7.52798901120157 --trim5 9 -i C,1.86307743581086 --rfg 38.3822187597345,13.8510468324362 --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1118s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1118s 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 1118s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s Read 50 alignments... 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1118s 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 1118s Read 100 alignments... 1118s 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 1118s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1118s 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 1118s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 1118s 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 1118s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (1) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 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 1118s 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 1118s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 1118s 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 1118s Warning: skipping read 'R_1_1_1_141_141_1/1' because length (0) <= # seed mismatches (0) 1118s Warning: skipping read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 1118s 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 1118s 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 1118s 143 reads; of these: 1118s 143 (100.00%) were unpaired; of these: 1118s 131 (91.61%) aligned 0 times 1118s 2 (1.40%) aligned exactly 1 time 1118s 10 (6.99%) aligned >1 times 1118s 8.39% overall alignment rate 1118s Read 150 alignments... 1118s Read 200 alignments... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s GGA 1118s GGA 1118s Processing line... 1118s GGA 1118s GGA 1118s Processing line... 1118s GGA 1118s GGA 1118s Processing line... 1118s GGA 1118s GGA 1118s Processing line... 1118s GGA 1118s GGA 1118s Processing line... 1118s GGA 1118s GGA 1118s Processing line... 1118s GGA 1118s GGA 1118s Processing line... 1118s GGA 1118s GGA 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s CAG 1118s CAG 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s ACGAGCCTGTCACATCGAGAT 1118s ACGAGCCTGTCACATCGAGAT 1118s Processing line... 1118s ACGAGCCTGTCACATCGAGAT 1118s ACGAGCCTGTCACATCGAGAT 1118s Processing line... 1118s ACGAGCCTGTCACATCGAGAT 1118s ACGAGCCTGTCACATCGAGAT 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s GTG 1118s GTG 1118s Processing line... 1118s GTG 1118s GTG 1118s Processing line... 1118s GTG 1118s GTG 1118s Processing line... 1118s GTG 1118s GTG 1118s Processing line... 1118s GTG 1118s GTG 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s TGG 1118s TGG 1118s Processing line... 1118s TGG 1118s TGG 1118s Processing line... 1118s TGG 1118s TGG 1118s Processing line... 1118s TGG 1118s TGG 1118s Processing line... 1118s TGG 1118s TGG 1118s Processing line... 1118s TGG 1118s TGG 1118s Processing line... 1118s TGG 1118s TGG 1118s Processing line... 1118s TGG 1118s TGG 1118s Processing line... 1118s TGG 1118s TGG 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s AA 1118s AA 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s GGTC 1118s GGTC 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s CACC 1118s CACC 1118s Processing line... 1118s CACC 1118s CACC 1118s Processing line... 1118s CACC 1118s CACC 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s GATAACC 1118s GATAACC 1118s Processing line... 1118s GATAACC 1118s GATAACC 1118s Processing line... 1118s GATAACC 1118s GATAACC 1118s Processing line... 1118s GATAACC 1118s GATAACC 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s TC 1118s TC 1118s Processing line... 1118s TC 1118s TC 1118s Processing line... 1118s TC 1118s TC 1118s Processing line... 1118s TC 1118s TC 1118s Processing line... 1118s TC 1118s TC 1118s Processing line... 1118s TC 1118s TC 1118s Processing line... 1118s TC 1118s TC 1118s Processing line... 1118s TC 1118s TC 1118s Processing line... 1118s TC 1118s TC 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s AT 1118s AT 1118s Processing line... 1118s AT 1118s AT 1118s Processing line... 1118s AT 1118s AT 1118s Processing line... 1118s AT 1118s AT 1118s Processing line... 1118s AT 1118s AT 1118s Processing line... 1118s AT 1118s AT 1118s Processing line... 1118s AT 1118s AT 1118s Processing line... 1118s AT 1118s AT 1118s Processing line... 1118s AT 1118s AT 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s Processing line... 1118s --- Summary --- 1118s Read 1 reference strings 1118s Checked 70 alignments, 0 edits 1118s --------------- 1118s PASSED 1118s ALSO checking that bowtie2 and bowtie2-align match up 1118s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --ma 2.79945143542875 --large-index -k 9 --rdg 11.4573630289528 -N 0 -L22 -R 2 -D 47 --nofw --np 4 --n-ceil 1.1628031131524,0.914145545662554 --score-min L,3.21375200672491,7.52798901120157 --trim5 9 -i C,1.86307743581086 --rfg 38.3822187597345,13.8510468324362 --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1119s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1119s 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 1119s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 1119s 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 1119s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 1119s 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 1119s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (1) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 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 1119s 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 1119s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 1119s 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 1119s Warning: skipping read 'R_1_1_1_141_141_1/1' because length (0) <= # seed mismatches (0) 1119s Warning: skipping read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 1119s 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 1119s 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 1119s 143 reads; of these: 1119s 143 (100.00%) were unpaired; of these: 1119s 131 (91.61%) aligned 0 times 1119s 2 (1.40%) aligned exactly 1 time 1119s 10 (6.99%) aligned >1 times 1119s 8.39% overall alignment rate 1119s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1119s Flattened IUPAC characters 1119s Mutating sequence Sim.pm.1 1119s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1119s Finished SNPs 1119s Finished ref gaps 1119s Finished read gaps 1119s Mutating sequence Sim.pm.2 1119s Introducing 1 SNPs, 4/1 ref/read gaps, and 1 rearrangements 1119s Finished SNPs 1119s Finished ref gaps 1119s Finished read gaps 1119s Mutated reference genome to subject genome 1119s SNPs introduced: 2 1119s Reference gaps introduced: 4 1119s Read gaps introduced: 1 1119s Rearrangements introduced: 1 1119s Created read sampler 1119s Sampling 62 reads 1119s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1119s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1119s parsing sequence Sim.pm.1... 1119s parsing sequence Sim.pm.2... 1119s Parsed 269 reference bases 1119s *** Run 2 of 100 1119s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --mp 2.83713374946097,2.56118834330747 --local --large-index --np 5 --nofw --rfg 1.95057822940832,16.3370161366865 --n-ceil 0.102863316304694,0.234160691687678 --score-min L,7.86768157209872,2.14916894476831 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1119s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 1119s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1119s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 1119s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1119s 62 reads; of these: 1119s 62 (100.00%) were paired; of these: 1119s 62 (100.00%) aligned concordantly 0 times 1119s 0 (0.00%) aligned concordantly exactly 1 time 1119s 0 (0.00%) aligned concordantly >1 times 1119s ---- 1119s 62 pairs aligned concordantly 0 times; of these: 1119s 0 (0.00%) aligned discordantly 1 time 1119s ---- 1119s 62 pairs aligned 0 times concordantly or discordantly; of these: 1119s 124 mates make up the pairs; of these: 1119s 124 (100.00%) aligned 0 times 1119s 0 (0.00%) aligned exactly 1 time 1119s 0 (0.00%) aligned >1 times 1119s 0.00% overall alignment rate 1119s Read 50 alignments... 1119s Read 100 alignments... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --mp 2.83713374946097,2.56118834330747 --local --large-index --np 5 --nofw --rfg 1.95057822940832,16.3370161366865 --n-ceil 0.102863316304694,0.234160691687678 --score-min L,7.86768157209872,2.14916894476831 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s Processing line... 1119s --- Summary --- 1119s Read 1 reference strings 1119s Checked 0 alignments, 0 edits 1119s --------------- 1119s PASSED 1119s ALSO checking that bowtie2 and bowtie2-align match up 1119s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 1119s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1119s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 1119s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1119s 62 reads; of these: 1119s 62 (100.00%) were paired; of these: 1119s 62 (100.00%) aligned concordantly 0 times 1119s 0 (0.00%) aligned concordantly exactly 1 time 1119s 0 (0.00%) aligned concordantly >1 times 1119s ---- 1119s 62 pairs aligned concordantly 0 times; of these: 1119s 0 (0.00%) aligned discordantly 1 time 1119s ---- 1119s 62 pairs aligned 0 times concordantly or discordantly; of these: 1119s 124 mates make up the pairs; of these: 1119s 124 (100.00%) aligned 0 times 1119s 0 (0.00%) aligned exactly 1 time 1119s 0 (0.00%) aligned >1 times 1119s 0.00% overall alignment rate 1119s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1119s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1119s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --mp 2.83713374946097,2.56118834330747 --local --large-index --np 5 --nofw --rfg 1.95057822940832,16.3370161366865 --n-ceil 0.102863316304694,0.234160691687678 --score-min L,7.86768157209872,2.14916894476831 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1120s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 1120s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1120s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 1120s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1120s 62 reads; of these: 1120s 62 (100.00%) were paired; of these: 1120s 62 (100.00%) aligned concordantly 0 times 1120s 0 (0.00%) aligned concordantly exactly 1 time 1120s 0 (0.00%) aligned concordantly >1 times 1120s ---- 1120s 62 pairs aligned concordantly 0 times; of these: 1120s 0 (0.00%) aligned discordantly 1 time 1120s ---- 1120s 62 pairs aligned 0 times concordantly or discordantly; of these: 1120s 124 mates make up the pairs; of these: 1120s 124 (100.00%) aligned 0 times 1120s 0 (0.00%) aligned exactly 1 time 1120s 0 (0.00%) aligned >1 times 1120s 0.00% overall alignment rate 1120s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1120s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1120s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1120s Flattened IUPAC characters 1120s Mutating sequence Sim.pm.1 1120s Introducing 9 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1120s Finished SNPs 1120s Finished ref gaps 1120s Finished read gaps 1120s Mutating sequence Sim.pm.2 1120s Introducing 17 SNPs, 0/1 ref/read gaps, and 2 rearrangements 1120s Finished SNPs 1120s Finished ref gaps 1120s Finished read gaps 1120s Mutated reference genome to subject genome 1120s SNPs introduced: 26 1120s Reference gaps introduced: 1 1120s Read gaps introduced: 2 1120s Rearrangements introduced: 2 1120s Created read sampler 1120s Sampling 47 reads 1120s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1120s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1120s parsing sequence Sim.pm.1... 1120s *** Run 3 of 100 1120s /usr/bin/bowtie2 --large-index --local --mp 6.53496457704901,2.34563002985835 --rdg 23.1185494973681,14.578153767224 --cp-ival 1 --mm --cp-min 5 --score-min L,2.83257896442395,7.67503421957507 --gbar 2 --rfg 10.0144927144199 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1120s parsing sequence Sim.pm.2... 1120s Parsed 269 reference bases 1120s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 1120s Warning: skipping mate #2 of read '34' because it was < 2 characters long 1120s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 1120s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1120s 47 reads; of these: 1120s 47 (100.00%) were paired; of these: 1120s 47 (100.00%) aligned concordantly 0 times 1120s 0 (0.00%) aligned concordantly exactly 1 time 1120s 0 (0.00%) aligned concordantly >1 times 1120s ---- 1120s 47 pairs aligned concordantly 0 times; of these: 1120s 0 (0.00%) aligned discordantly 1 time 1120s ---- 1120s 47 pairs aligned 0 times concordantly or discordantly; of these: 1120s 94 mates make up the pairs; of these: 1120s 94 (100.00%) aligned 0 times 1120s 0 (0.00%) aligned exactly 1 time 1120s 0 (0.00%) aligned >1 times 1120s 0.00% overall alignment rate 1120s Read 50 alignments... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s --- Summary --- 1120s Read 1 reference strings 1120s Checked 0 alignments, 0 edits 1120s --------------- 1120s PASSED 1120s Flattened IUPAC characters 1120s Mutating sequence Sim.pm.1 1120s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1120s Finished SNPs 1120s Finished ref gaps 1120s Finished read gaps 1120s Mutating sequence Sim.pm.2 1120s Introducing 28 SNPs, 3/0 ref/read gaps, and 3 rearrangements 1120s Finished SNPs 1120s Finished ref gaps 1120s Finished read gaps 1120s Mutated reference genome to subject genome 1120s SNPs introduced: 34 1120s Reference gaps introduced: 3 1120s Read gaps introduced: 0 1120s Rearrangements introduced: 3 1120s Created read sampler 1120s Sampling 90 reads 1120s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1120s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1120s parsing sequence Sim.pm.1... 1120s parsing sequence Sim.pm.2... 1120s Parsed 269 reference bases 1120s *** Run 4 of 100 1120s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mp 4.83651221222409,1.04840353136617 --large-index -k 7 --nofw -N 0 -L21 -R 1 --rfg 47.3423502641263,13.1762204677699 --n-ceil 1.02911756023531,0.772037285437421 --score-min L,1.50849486897796,2.46874417450431 -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1120s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1120s 90 reads; of these: 1120s 90 (100.00%) were unpaired; of these: 1120s 82 (91.11%) aligned 0 times 1120s 1 (1.11%) aligned exactly 1 time 1120s 7 (7.78%) aligned >1 times 1120s 8.89% overall alignment rate 1120s Read 50 alignments... 1120s Read 100 alignments... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s TCA 1120s TCA 1120s Processing line... 1120s TCA 1120s TCA 1120s Processing line... 1120s TCA 1120s TCA 1120s Processing line... 1120s GAACACGAGCC 1120s GAACACGAGCC 1120s Processing line... 1120s GAACACGAGCC 1120s GAACACGAGCC 1120s Processing line... 1120s GAACACGAGCC 1120s GAACACGAGCC 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s GGGGTATG 1120s GGGGTATG 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s AGCCTGTCACATCGAGATGGACCACCTCGTG 1120s AGCCTGTCACATCGAGATGGACCACCTCGTG 1120s Processing line... 1120s AGCCTGTCACATCGAGATGGACCACCTCGTG 1120s AGCCTGTCACATCGAGATGGACCACCTCGTG 1120s Processing line... 1120s AGCCTGTCACATCGAGATGGACCACCTCGTG 1120s AGCCTGTCACATCGAGATGGACCACCTCGTG 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s GTC 1120s GTC 1120s Processing line... 1120s GTC 1120s GTC 1120s Processing line... 1120s GTC 1120s GTC 1120s Processing line... 1120s GTC 1120s GTC 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s ACACGAGC 1120s ACACGAGC 1120s Processing line... 1120s ACACGAGC 1120s ACACGAGC 1120s Processing line... 1120s ACACGAGC 1120s ACACGAGC 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s CG 1120s CG 1120s Processing line... 1120s CG 1120s CG 1120s Processing line... 1120s CG 1120s CG 1120s Processing line... 1120s CG 1120s CG 1120s Processing line... 1120s CG 1120s CG 1120s Processing line... 1120s CG 1120s CG 1120s Processing line... 1120s CG 1120s CG 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s Processing line... 1120s ATCGAG 1120s ATCGAG 1120s Processing line... 1120s ATCGAG 1120s ATCGAG 1120s Processing line... 1120s ATCGAG 1120s ATCGAG 1120s --- Summary --- 1120s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mp 4.83651221222409,1.04840353136617 --large-index -k 7 --nofw -N 0 -L21 -R 1 --rfg 47.3423502641263,13.1762204677699 --n-ceil 1.02911756023531,0.772037285437421 --score-min L,1.50849486897796,2.46874417450431 -r -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1120s Read 1 reference strings 1120s Checked 27 alignments, 0 edits 1120s --------------- 1120s PASSED 1120s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1121s 90 reads; of these: 1121s 90 (100.00%) were unpaired; of these: 1121s 82 (91.11%) aligned 0 times 1121s 1 (1.11%) aligned exactly 1 time 1121s 7 (7.78%) aligned >1 times 1121s 8.89% overall alignment rate 1121s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1121s Flattened IUPAC characters 1121s Mutating sequence Sim.pm.1 1121s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1121s Finished SNPs 1121s Finished ref gaps 1121s Finished read gaps 1121s Mutating sequence Sim.pm.2 1121s Introducing 22 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1121s Finished SNPs 1121s Finished ref gaps 1121s Finished read gaps 1121s Mutated reference genome to subject genome 1121s SNPs introduced: 30 1121s Reference gaps introduced: 1 1121s Read gaps introduced: 0 1121s Rearrangements introduced: 0 1121s Created read sampler 1121s Sampling 32 reads 1121s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1121s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1121s parsing sequence Sim.pm.1... 1121s parsing sequence Sim.pm.2... 1121s *** Run 5 of 100 1121s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --mp 5.2779879624159,4.41949038890036 --rdg 47.6923809008917 --local --large-index -N 1 -L17 --trim5 0 -i S,0.458908887117754 --rfg 7.16994493801394 --score-min L,4.67495935380997,9.21054995334556 --gbar 5 -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw 1121s Parsed 269 reference bases 1121s Warning: skipping read '6' because length (1) <= # seed mismatches (1) 1121s Warning: skipping read '6' because it was < 2 characters long 1121s 32 reads; of these: 1121s 32 (100.00%) were unpaired; of these: 1121s 32 (100.00%) aligned 0 times 1121s 0 (0.00%) aligned exactly 1 time 1121s 0 (0.00%) aligned >1 times 1121s 0.00% overall alignment rate 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s --- Summary --- 1121s Read 1 reference strings 1121s Checked 0 alignments, 0 edits 1121s --------------- 1121s PASSED 1121s Flattened IUPAC characters 1121s Mutating sequence Sim.pm.1 1121s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1121s Finished SNPs 1121s Finished ref gaps 1121s Finished read gaps 1121s Mutating sequence Sim.pm.2 1121s Introducing 20 SNPs, 0/1 ref/read gaps, and 2 rearrangements 1121s Finished SNPs 1121s Finished ref gaps 1121s Finished read gaps 1121s Mutated reference genome to subject genome 1121s SNPs introduced: 20 1121s Reference gaps introduced: 0 1121s Read gaps introduced: 1 1121s Rearrangements introduced: 3 1121s Created read sampler 1121s Sampling 129 reads 1121s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1121s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1121s parsing sequence Sim.pm.1... 1121s parsing sequence Sim.pm.2... 1121s Parsed 269 reference bases 1121s *** Run 6 of 100 1121s /usr/bin/bowtie2 --rfg 46.9017510761734 --rdg 35.9332578905518 --trim3 1 -k 4 --score-min L,6.04202252280522,2.43156841661935 --large-index --nofw --np 4 --cp-min 3 --cp-ival 3 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1121s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1121s Warning: skipping read '39' because it was < 2 characters long 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1121s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 1121s Warning: skipping read '66' because it was < 2 characters long 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1121s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1121s Warning: skipping read '86' because it was < 2 characters long 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1121s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1121s Warning: skipping read '91' because it was < 2 characters long 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1121s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 1121s Warning: skipping read '94' because it was < 2 characters long 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1121s Read 50 alignments... 1121s Read 100 alignments... 1121s 129 reads; of these: 1121s 129 (100.00%) were unpaired; of these: 1121s 113 (87.60%) aligned 0 times 1121s 7 (5.43%) aligned exactly 1 time 1121s 9 (6.98%) aligned >1 times 1121s 12.40% overall alignment rate 1121s Read 150 alignments... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s TGGTGAGGGTCGAGGAC 1121s TGGTGAGGGTCGAGGAC 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s CTG 1121s CTG 1121s Processing line... 1121s CTG 1121s CTG 1121s Processing line... 1121s CTG 1121s CTG 1121s Processing line... 1121s CTG 1121s CTG 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s GG 1121s GG 1121s Processing line... 1121s GG 1121s GG 1121s Processing line... 1121s GG 1121s GG 1121s Processing line... 1121s GG 1121s GG 1121s Processing line... 1121s GATGGACCACCTCGTG 1121s GATGGACCACCTCGTG 1121s Processing line... 1121s GATGGACCACCTCGTG 1121s GATGGACCACCTCGTG 1121s Processing line... 1121s GATGGACCACCTCGTG 1121s GATGGACCACCTCGTG 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s CCTCGT 1121s CCTCGT 1121s Processing line... 1121s CCTCGT 1121s CCTCGT 1121s Processing line... 1121s CCTCGT 1121s CCTCGT 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s GG 1121s GG 1121s Processing line... 1121s GG 1121s GG 1121s Processing line... 1121s GG 1121s GG 1121s Processing line... 1121s GG 1121s GG 1121s Processing line... 1121s TAG 1121s TAG 1121s Processing line... 1121s TAG 1121s TAG 1121s Processing line... 1121s TAG 1121s TAG 1121s Processing line... 1121s TAG 1121s TAG 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s GGTCGAG 1121s GGTCGAG 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s AGAACA 1121s AGAACA 1121s Processing line... 1121s AGAACA 1121s AGAACA 1121s Processing line... 1121s AGAACA 1121s AGAACA 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s CTCG 1121s CTCG 1121s Processing line... 1121s CTCG 1121s CTCG 1121s Processing line... 1121s CTCG 1121s CTCG 1121s Processing line... 1121s CTCG 1121s CTCG 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s CTCGCAGCG 1121s CTCGCAGCG 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s GT 1121s GT 1121s Processing line... 1121s GT 1121s GT 1121s Processing line... 1121s GT 1121s GT 1121s Processing line... 1121s GT 1121s GT 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s AGCGCG 1121s AGCGCG 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s GGGTCGAGG 1121s GGGTCGAGG 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s Processing line... 1121s ACCAAAAC 1121s ACCAAAAC 1121s Processing line... 1121s Processing line... 1121s TGGCTGAG 1121s TGGCTGAG 1121s Processing line... 1121s --- Summary --- 1121s Read 1 reference strings 1121s Checked 40 alignments, 0 edits 1121s --------------- 1121s PASSED 1121s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1121s /usr/bin/bowtie2 --rfg 46.9017510761734 --rdg 35.9332578905518 --trim3 1 -k 4 --score-min L,6.04202252280522,2.43156841661935 --large-index --nofw --np 4 --cp-min 3 --cp-ival 3 -f -p 2 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1121s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1122s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1122s Warning: skipping read '39' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1122s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '66' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1122s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1122s Warning: skipping read '86' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1122s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1122s Warning: skipping read '91' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1122s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '94' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1122s 129 reads; of these: 1122s 129 (100.00%) were unpaired; of these: 1122s 113 (87.60%) aligned 0 times 1122s 7 (5.43%) aligned exactly 1 time 1122s 9 (6.98%) aligned >1 times 1122s 12.40% overall alignment rate 1122s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1122s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1122s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1122s Flattened IUPAC characters 1122s Mutating sequence Sim.pm.2 1122s Introducing 0 SNPs, 0/5 ref/read gaps, and 1 rearrangements 1122s Finished SNPs 1122s Finished ref gaps 1122s Finished read gaps 1122s Mutating sequence Sim.pm.1 1122s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1122s Finished SNPs 1122s Finished ref gaps 1122s Finished read gaps 1122s Mutated reference genome to subject genome 1122s SNPs introduced: 4 1122s Reference gaps introduced: 0 1122s Read gaps introduced: 6 1122s Rearrangements introduced: 2 1122s Created read sampler 1122s Sampling 188 reads 1122s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1122s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1122s parsing sequence Sim.pm.1... 1122s parsing sequence Sim.pm.2... 1122s Parsed 269 reference bases 1122s *** Run 7 of 100 1122s /usr/bin/bowtie2 --mp 9.74610402501134,4.78057779620826 --ma 28.9071076657177 --large-index --score-min L,1.70564296002484,1.06905133643624 --cp-min 6 --nofw --cp-ival 1 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1122s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1122s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '30' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1122s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '40' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1122s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '44' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1122s Warning: skipping read '112' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '112' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 1122s Read 50 alignments... 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 1122s Read 100 alignments... 1122s 188 reads; of these: 1122s 188 (100.00%) were unpaired; of these: 1122s 160 (85.11%) aligned 0 times 1122s 5 (2.66%) aligned exactly 1 time 1122s 23 (12.23%) aligned >1 times 1122s 14.89% overall alignment rate 1122s Read 150 alignments... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s AGTAGAACACGAGCCTGTCA 1122s AGTAGAACACGAGCCTGTCA 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s TGGTGAGGGTCG 1122s TGGTGAGGGTCG 1122s Processing line... 1122s Processing line... 1122s CCT 1122s CCT 1122s Processing line... 1122s TG 1122s TG 1122s Processing line... 1122s Processing line... 1122s AGTA 1122s AGTA 1122s Processing line... 1122s Processing line... 1122s AGA 1122s AGA 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s GT 1122s GT 1122s Processing line... 1122s Processing line... 1122s AGA 1122s AGA 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s GAAC 1122s GAAC 1122s Processing line... 1122s TGAA 1122s TGAA 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s ACCTCGTGG 1122s ACCTCGTGG 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s CTCGT 1122s CTCGT 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s GATGGACCACCTCGTGGG 1122s GATGGACCACCTCGTGGG 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s CCT 1122s CCT 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s AGATGGACCA 1122s AGATGGACCA 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s GA 1122s GA 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s CGG 1122s CGG 1122s Processing line... 1122s GAT 1122s GAT 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s GTCACATC 1122s GTCACATC 1122s Processing line... 1122s Processing line... 1122s GAT 1122s GAT 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s AACG 1122s AACG 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s CC 1122s CC 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s AGTAGAACACGAGCCTGT 1122s AGTAGAACACGAGCCTGT 1122s Processing line... 1122s Processing line... 1122s CGAGCCTGTCACATCGAG 1122s CGAGCCTGTCACATCGAG 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s CGAGCCTGTCACATCGAGATGGACCA 1122s CGAGCCTGTCACATCGAGATGGACCA 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s TCGAC 1122s TCGAC 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s GAT 1122s GAT 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s CGAG 1122s CGAG 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s Processing line... 1122s --- Summary --- 1122s Read 1 reference strings 1122s Checked 28 alignments, 0 edits 1122s --------------- 1122s PASSED 1122s ALSO checking that bowtie2 and bowtie2-align match up 1122s /usr/bin/bowtie2 --mp 9.74610402501134,4.78057779620826 --ma 28.9071076657177 --large-index --score-min L,1.70564296002484,1.06905133643624 --cp-min 6 --nofw --cp-ival 1 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1122s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1122s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '30' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1122s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '40' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1122s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '44' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1122s Warning: skipping read '112' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '112' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 1122s 188 reads; of these: 1122s 188 (100.00%) were unpaired; of these: 1122s 160 (85.11%) aligned 0 times 1122s 5 (2.66%) aligned exactly 1 time 1122s 23 (12.23%) aligned >1 times 1122s 14.89% overall alignment rate 1122s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1122s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1122s /usr/bin/bowtie2 --mp 9.74610402501134,4.78057779620826 --ma 28.9071076657177 --large-index --score-min L,1.70564296002484,1.06905133643624 --cp-min 6 --nofw --cp-ival 1 -f -p 4 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1122s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1122s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '30' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1122s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '40' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1122s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '44' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1122s Warning: skipping read '112' because length (1) <= # seed mismatches (0) 1122s Warning: skipping read '112' because it was < 2 characters long 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 1122s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 1123s 188 reads; of these: 1123s 188 (100.00%) were unpaired; of these: 1123s 160 (85.11%) aligned 0 times 1123s 5 (2.66%) aligned exactly 1 time 1123s 23 (12.23%) aligned >1 times 1123s 14.89% overall alignment rate 1123s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1123s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1123s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1123s *** Run 8 of 100 1123s /usr/bin/bowtie2 -M 2 --large-index --local --mp 7.13413288323269,1.98990863754518 --trim3 1 --mm --cp-ival 1 --cp-min 5 --score-min L,4.19313934790755,1.40322658898042 --rfg 29.9552078448202 -D 35 -N 1 -L26 --norc -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1123s Flattened IUPAC characters 1123s Mutating sequence Sim.pm.1 1123s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1123s Finished SNPs 1123s Finished ref gaps 1123s Finished read gaps 1123s Mutating sequence Sim.pm.2 1123s Introducing 10 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1123s Finished SNPs 1123s Finished ref gaps 1123s Finished read gaps 1123s Mutated reference genome to subject genome 1123s SNPs introduced: 11 1123s Reference gaps introduced: 0 1123s Read gaps introduced: 0 1123s Rearrangements introduced: 2 1123s Created read sampler 1123s Sampling 57 reads 1123s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1123s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1123s parsing sequence Sim.pm.1... 1123s parsing sequence Sim.pm.2... 1123s Parsed 269 reference bases 1123s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1123s Warning: skipping read '28' because length (1) <= # seed mismatches (1) 1123s Warning: skipping read '28' because it was < 2 characters long 1123s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 1123s Warning: skipping read '30' because it was < 2 characters long 1123s Warning: skipping read '35' because length (1) <= # seed mismatches (1) 1123s Warning: skipping read '35' because it was < 2 characters long 1123s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 1123s Warning: skipping read '47' because it was < 2 characters long 1123s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 1123s Warning: skipping read '54' because it was < 2 characters long 1123s 57 reads; of these: 1123s 57 (100.00%) were unpaired; of these: 1123s 50 (87.72%) aligned 0 times 1123s 1 (1.75%) aligned exactly 1 time 1123s 6 (10.53%) aligned >1 times 1123s 12.28% overall alignment rate 1123s Read 50 alignments... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s AGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGATAA 1123s AGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAA 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s TCACATCGAGATGGACCACCTCGTGGGATGGATAACCAGAGTAGA 1123s TCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGA 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s ACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATAACCATAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGCGAACCAAAACGC 1123s ANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAACGC 1123s Processing line... 1123s TAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATGACGACAGTA 1123s TAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTA 1123s Processing line... 1123s Processing line... 1123s GAGCCTGTCACATCGAGA 1123s GAGCCTGTCACATCGAGA 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s GTCACATCGAGATGGACCACCTCGTGGGATGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGG------A 1123s GTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATA 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s CGAGATGGACCACCTCGTG 1123s CGAGATGGACCACCTCGTG 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s --- Summary --- 1123s Read 1 reference strings 1123s Checked 7 alignments, 0 edits 1123s --------------- 1123s PASSED 1123s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1123s /usr/bin/bowtie2 -M 2 --large-index --local --mp 7.13413288323269,1.98990863754518 --trim3 1 --mm --cp-ival 1 --cp-min 5 --score-min L,4.19313934790755,1.40322658898042 --rfg 29.9552078448202 -D 35 -N 1 -L26 --norc -f -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1123s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1123s Warning: skipping read '35' because length (1) <= # seed mismatches (1) 1123s Warning: skipping read '35' because it was < 2 characters long 1123s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 1123s Warning: skipping read '54' because it was < 2 characters long 1123s Warning: skipping read '28' because length (1) <= # seed mismatches (1) 1123s Warning: skipping read '28' because it was < 2 characters long 1123s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 1123s Warning: skipping read '30' because it was < 2 characters long 1123s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 1123s Warning: skipping read '47' because it was < 2 characters long 1123s 57 reads; of these: 1123s 57 (100.00%) were unpaired; of these: 1123s 50 (87.72%) aligned 0 times 1123s 1 (1.75%) aligned exactly 1 time 1123s 6 (10.53%) aligned >1 times 1123s 12.28% overall alignment rate 1123s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1123s Flattened IUPAC characters 1123s Mutating sequence Sim.pm.2 1123s Introducing 13 SNPs, 2/0 ref/read gaps, and 2 rearrangements 1123s Finished SNPs 1123s Finished ref gaps 1123s Finished read gaps 1123s Mutating sequence Sim.pm.1 1123s Introducing 1 SNPs, 1/0 ref/read gaps, and 2 rearrangements 1123s Finished SNPs 1123s Finished ref gaps 1123s Finished read gaps 1123s Mutated reference genome to subject genome 1123s SNPs introduced: 14 1123s Reference gaps introduced: 3 1123s Read gaps introduced: 0 1123s Rearrangements introduced: 4 1123s Created read sampler 1123s Sampling 122 reads 1123s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1123s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1123s parsing sequence Sim.pm.1... 1123s parsing sequence Sim.pm.2... 1123s Parsed 269 reference bases 1123s *** Run 9 of 100 1123s /usr/bin/bowtie2 --norc --np 2 --gbar 1 --score-min L,9.10770758062375,8.64036688973717 --rfg 17.7768308487863,1.85592002875786 --trim5 4 --mm --cp-ival 2 --cp-min 5 --large-index --local --rdg 44.3324456053124 --mp 2.57146477493202,1.06398379264335 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1123s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1123s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1123s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '48' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '64' because it was < 2 characters long 1123s Read 50 alignments... 1123s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1123s Read 100 alignments... 1123s Warning: skipping mate #2 of read '106' because length (1) <= # seed mismatches (0) 1123s Warning: skipping mate #2 of read '106' because it was < 2 characters long 1123s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '109' because it was < 2 characters long 1123s Read 150 alignments... 1123s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 1123s Warning: skipping mate #1 of read '120' because it was < 2 characters long 1123s 122 reads; of these: 1123s 108 (88.52%) were paired; of these: 1123s 108 (100.00%) aligned concordantly 0 times 1123s 0 (0.00%) aligned concordantly exactly 1 time 1123s 0 (0.00%) aligned concordantly >1 times 1123s ---- 1123s 108 pairs aligned concordantly 0 times; of these: 1123s 0 (0.00%) aligned discordantly 1 time 1123s ---- 1123s 108 pairs aligned 0 times concordantly or discordantly; of these: 1123s 216 mates make up the pairs; of these: 1123s 216 (100.00%) aligned 0 times 1123s 0 (0.00%) aligned exactly 1 time 1123s 0 (0.00%) aligned >1 times 1123s 14 (11.48%) were unpaired; of these: 1123s 14 (100.00%) aligned 0 times 1123s 0 (0.00%) aligned exactly 1 time 1123s 0 (0.00%) aligned >1 times 1123s 0.00% overall alignment rate 1123s Read 200 alignments... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s Processing line... 1123s --- Summary --- 1123s Read 1 reference strings 1123s Checked 0 alignments, 0 edits 1123s --------------- 1123s PASSED 1123s Flattened IUPAC characters 1123s Mutating sequence Sim.pm.1 1123s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1123s Finished SNPs 1123s Finished ref gaps 1123s Finished read gaps 1123s Mutating sequence Sim.pm.2 1123s Introducing 31 SNPs, 0/1 ref/read gaps, and 2 rearrangements 1123s Finished SNPs 1123s Finished ref gaps 1123s Finished read gaps 1123s Mutated reference genome to subject genome 1123s SNPs introduced: 31 1123s Reference gaps introduced: 0 1123s Read gaps introduced: 1 1123s Rearrangements introduced: 2 1123s Created read sampler 1123s Sampling 106 reads 1123s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1123s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1123s parsing sequence Sim.pm.1... 1123s parsing sequence Sim.pm.2... 1123s Parsed 269 reference bases 1123s *** Run 10 of 100 1123s /usr/bin/bowtie2 --large-index -M 5 --rdg 5.06712616361013 --cp-ival 1 --cp-min 2 --n-ceil 0.644633654874685,0.0819728488417772 --score-min L,2.75397051874897,6.50614710665425 --rfg 24.8783914072734 -i C,2.65030605731346 -N 1 -L20 -R 1 -D 12 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1123s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1124s Warning: skipping read '86' because length (1) <= # seed mismatches (1) 1124s Warning: skipping read '86' because it was < 2 characters long 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1124s 106 reads; of these: 1124s 106 (100.00%) were unpaired; of these: 1124s 89 (83.96%) aligned 0 times 1124s 3 (2.83%) aligned exactly 1 time 1124s 14 (13.21%) aligned >1 times 1124s 16.04% overall alignment rate 1124s Read 50 alignments... 1124s Read 100 alignments... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s GG 1124s GG 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s AAG 1124s AAG 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s GATAACC 1124s GATAACC 1124s Processing line... 1124s CTGTC 1124s CTGTC 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s CCTGT 1124s CCTGT 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s CCTGT 1124s CCTGT 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s GAGATG 1124s GAGATG 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s GG 1124s GG 1124s Processing line... 1124s ACCT 1124s ACCT 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s AG 1124s AG 1124s Processing line... 1124s Processing line... 1124s CA 1124s CA 1124s Processing line... 1124s Processing line... 1124s CACATCGA 1124s CACATCGA 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s GGA 1124s GGA 1124s Processing line... 1124s Processing line... 1124s CGAGCCTGT 1124s CGAGCCTGT 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s GGCTGAGA 1124s GGCTGAGA 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s /usr/bin/bowtie2 --large-index -M 5 --rdg 5.06712616361013 --cp-ival 1 --cp-min 2 --n-ceil 0.644633654874685,0.0819728488417772 --score-min L,2.75397051874897,6.50614710665425 --rfg 24.8783914072734 -i C,2.65030605731346 -N 1 -L20 -R 1 -D 12 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s TATCG 1124s TATCG 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s AC 1124s AC 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s Processing line... 1124s --- Summary --- 1124s Read 1 reference strings 1124s Checked 17 alignments, 0 edits 1124s --------------- 1124s PASSED 1124s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1124s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1124s Warning: skipping read '86' because length (1) <= # seed mismatches (1) 1124s Warning: skipping read '86' because it was < 2 characters long 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1124s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1124s 106 reads; of these: 1124s 106 (100.00%) were unpaired; of these: 1124s 89 (83.96%) aligned 0 times 1124s 3 (2.83%) aligned exactly 1 time 1124s 14 (13.21%) aligned >1 times 1124s 16.04% overall alignment rate 1124s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1124s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1124s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1124s Flattened IUPAC characters 1124s Mutating sequence Sim.pm.2 1124s Introducing 18 SNPs, 3/1 ref/read gaps, and 1 rearrangements 1124s Finished SNPs 1124s Finished ref gaps 1124s Finished read gaps 1124s Mutating sequence Sim.pm.1 1124s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1124s Finished SNPs 1124s Finished ref gaps 1124s Finished read gaps 1124s Mutated reference genome to subject genome 1124s SNPs introduced: 20 1124s Reference gaps introduced: 3 1124s Read gaps introduced: 1 1124s Rearrangements introduced: 2 1124s Created read sampler 1124s Sampling 118 reads 1124s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1124s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1124s parsing sequence Sim.pm.1... 1124s parsing sequence Sim.pm.2... 1124s Parsed 269 reference bases 1124s *** Run 11 of 100 1124s /usr/bin/bowtie2 -k 2 --large-index --local --trim3 7 --cp-ival 1 --mm --cp-min 3 --score-min L,1.76028062013157,8.69578897866517 --n-ceil 0.000965600173024468,1.30423931724408 -i C,2.53151317135367 --np 11 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1125s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1125s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1125s Warning: skipping read '20' because it was < 2 characters long 1125s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 1125s Warning: skipping read '24' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '48' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1125s Read 50 alignments... 1125s Read 100 alignments... 1125s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '71' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '80' because it was < 2 characters long 1125s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1125s Warning: skipping read '87' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '91' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '96' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '106' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #2 of read '110' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '110' because it was < 2 characters long 1125s Warning: skipping mate #2 of read '110' because it was < 2 characters long 1125s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 1125s Warning: skipping read '118' because it was < 2 characters long 1125s 118 reads; of these: 1125s 105 (88.98%) were paired; of these: 1125s 105 (100.00%) aligned concordantly 0 times 1125s 0 (0.00%) aligned concordantly exactly 1 time 1125s 0 (0.00%) aligned concordantly >1 times 1125s ---- 1125s 105 pairs aligned concordantly 0 times; of these: 1125s 0 (0.00%) aligned discordantly 1 time 1125s ---- 1125s 105 pairs aligned 0 times concordantly or discordantly; of these: 1125s 210 mates make up the pairs; of these: 1125s 210 (100.00%) aligned 0 times 1125s 0 (0.00%) aligned exactly 1 time 1125s 0 (0.00%) aligned >1 times 1125s 13 (11.02%) were unpaired; of these: 1125s 13 (100.00%) aligned 0 times 1125s 0 (0.00%) aligned exactly 1 time 1125s 0 (0.00%) aligned >1 times 1125s 0.00% overall alignment rate 1125s Read 150 alignments... 1125s Read 200 alignments... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s --- Summary --- 1125s Read 1 reference strings 1125s Checked 0 alignments, 0 edits 1125s --------------- 1125s PASSED 1125s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1125s /usr/bin/bowtie2 -k 2 --large-index --local --trim3 7 --cp-ival 1 --mm --cp-min 3 --score-min L,1.76028062013157,8.69578897866517 --n-ceil 0.000965600173024468,1.30423931724408 -i C,2.53151317135367 --np 11 -f -p 3 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1125s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1125s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1125s Warning: skipping read '20' because it was < 2 characters long 1125s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 1125s Warning: skipping read '24' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '48' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '61' because it was < 2 characters long 1125s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1125s Warning: skipping read '87' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '91' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '96' because it was < 2 characters long 1125s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 1125s Warning: skipping read '118' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '71' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '80' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '106' because it was < 2 characters long 1125s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 1125s Warning: skipping mate #2 of read '110' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '110' because it was < 2 characters long 1125s Warning: skipping mate #2 of read '110' because it was < 2 characters long 1125s 118 reads; of these: 1125s 105 (88.98%) were paired; of these: 1125s 105 (100.00%) aligned concordantly 0 times 1125s 0 (0.00%) aligned concordantly exactly 1 time 1125s 0 (0.00%) aligned concordantly >1 times 1125s ---- 1125s 105 pairs aligned concordantly 0 times; of these: 1125s 0 (0.00%) aligned discordantly 1 time 1125s ---- 1125s 105 pairs aligned 0 times concordantly or discordantly; of these: 1125s 210 mates make up the pairs; of these: 1125s 210 (100.00%) aligned 0 times 1125s 0 (0.00%) aligned exactly 1 time 1125s 0 (0.00%) aligned >1 times 1125s 13 (11.02%) were unpaired; of these: 1125s 13 (100.00%) aligned 0 times 1125s 0 (0.00%) aligned exactly 1 time 1125s 0 (0.00%) aligned >1 times 1125s 0.00% overall alignment rate 1125s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1125s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1125s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1125s Flattened IUPAC characters 1125s Mutating sequence Sim.pm.2 1125s Introducing 14 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1125s Finished SNPs 1125s Finished ref gaps 1125s Finished read gaps 1125s Mutating sequence Sim.pm.1 1125s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1125s Finished SNPs 1125s Finished ref gaps 1125s Finished read gaps 1125s Mutated reference genome to subject genome 1125s SNPs introduced: 15 1125s Reference gaps introduced: 2 1125s Read gaps introduced: 2 1125s Rearrangements introduced: 0 1125s Created read sampler 1125s Sampling 171 reads 1125s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1125s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1125s parsing sequence Sim.pm.1... 1125s parsing sequence Sim.pm.2... 1125s Parsed 269 reference bases 1125s *** Run 12 of 100 1125s /usr/bin/bowtie2 --large-index --score-min L,7.64533703068907,7.59459737480654 --local --rfg 7.61162097053034,6.69577669545124 --cp-ival 1 --cp-min 2 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1125s Read 50 alignments... 1125s Read 100 alignments... 1125s Read 150 alignments... 1125s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '123' because it was < 2 characters long 1125s Warning: skipping mate #2 of read '138' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #2 of read '138' because it was < 2 characters long 1125s Warning: skipping mate #2 of read '156' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #2 of read '156' because it was < 2 characters long 1125s Warning: skipping mate #2 of read '158' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #2 of read '158' because it was < 2 characters long 1125s Read 200 alignments... 1125s Read 250 alignments... 1125s Warning: skipping mate #1 of read '166' because length (1) <= # seed mismatches (0) 1125s Warning: skipping mate #1 of read '166' because it was < 2 characters long 1125s 171 reads; of these: 1125s 171 (100.00%) were paired; of these: 1125s 171 (100.00%) aligned concordantly 0 times 1125s 0 (0.00%) aligned concordantly exactly 1 time 1125s 0 (0.00%) aligned concordantly >1 times 1125s ---- 1125s 171 pairs aligned concordantly 0 times; of these: 1125s 0 (0.00%) aligned discordantly 1 time 1125s ---- 1125s 171 pairs aligned 0 times concordantly or discordantly; of these: 1125s 342 mates make up the pairs; of these: 1125s 342 (100.00%) aligned 0 times 1125s 0 (0.00%) aligned exactly 1 time 1125s 0 (0.00%) aligned >1 times 1125s 0.00% overall alignment rate 1125s Read 300 alignments... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing 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line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s Processing line... 1125s --- Summary --- 1125s Read 1 reference strings 1125s Checked 0 alignments, 0 edits 1125s --------------- 1125s PASSED 1125s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1125s /usr/bin/bowtie2 --large-index --score-min L,7.64533703068907,7.59459737480654 --local --rfg 7.61162097053034,6.69577669545124 --cp-ival 1 --cp-min 2 -f -p 2 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1126s Warning: skipping mate #2 of read '138' because length (1) <= # seed mismatches (0) 1126s Warning: skipping mate #2 of read '138' because it was < 2 characters long 1126s Warning: skipping mate #2 of read '156' because length (1) <= # seed mismatches (0) 1126s Warning: skipping mate #2 of read '156' because it was < 2 characters long 1126s Warning: skipping mate #2 of read '158' because length (1) <= # seed mismatches (0) 1126s Warning: skipping mate #2 of read '158' because it was < 2 characters long 1126s Warning: skipping mate #1 of read '166' because length (1) <= # seed mismatches (0) 1126s Warning: skipping mate #1 of read '166' because it was < 2 characters long 1126s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 1126s Warning: skipping mate #1 of read '123' because it was < 2 characters long 1126s 171 reads; of these: 1126s 171 (100.00%) were paired; of these: 1126s 171 (100.00%) aligned concordantly 0 times 1126s 0 (0.00%) aligned concordantly exactly 1 time 1126s 0 (0.00%) aligned concordantly >1 times 1126s ---- 1126s 171 pairs aligned concordantly 0 times; of these: 1126s 0 (0.00%) aligned discordantly 1 time 1126s ---- 1126s 171 pairs aligned 0 times concordantly or discordantly; of these: 1126s 342 mates make up the pairs; of these: 1126s 342 (100.00%) aligned 0 times 1126s 0 (0.00%) aligned exactly 1 time 1126s 0 (0.00%) aligned >1 times 1126s 0.00% overall alignment rate 1126s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1126s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1126s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1126s /usr/bin/bowtie2 --large-index --score-min L,7.64533703068907,7.59459737480654 --local --rfg 7.61162097053034,6.69577669545124 --cp-ival 1 --cp-min 2 -f -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1126s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1126s Warning: skipping mate #2 of read '138' because length (1) <= # seed mismatches (0) 1126s Warning: skipping mate #2 of read '138' because it was < 2 characters long 1126s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 1126s Warning: skipping mate #1 of read '123' because it was < 2 characters long 1126s Warning: skipping mate #2 of read '156' because length (1) <= # seed mismatches (0) 1126s Warning: skipping mate #2 of read '156' because it was < 2 characters long 1126s Warning: skipping mate #2 of read '158' because length (1) <= # seed mismatches (0) 1126s Warning: skipping mate #2 of read '158' because it was < 2 characters long 1126s Warning: skipping mate #1 of read '166' because length (1) <= # seed mismatches (0) 1126s Warning: skipping mate #1 of read '166' because it was < 2 characters long 1126s 171 reads; of these: 1126s 171 (100.00%) were paired; of these: 1126s 171 (100.00%) aligned concordantly 0 times 1126s 0 (0.00%) aligned concordantly exactly 1 time 1126s 0 (0.00%) aligned concordantly >1 times 1126s ---- 1126s 171 pairs aligned concordantly 0 times; of these: 1126s 0 (0.00%) aligned discordantly 1 time 1126s ---- 1126s 171 pairs aligned 0 times concordantly or discordantly; of these: 1126s 342 mates make up the pairs; of these: 1126s 342 (100.00%) aligned 0 times 1126s 0 (0.00%) aligned exactly 1 time 1126s 0 (0.00%) aligned >1 times 1126s 0.00% overall alignment rate 1126s Flattened IUPAC characters 1126s Mutating sequence Sim.pm.1 1126s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1126s Finished SNPs 1126s Finished ref gaps 1126s Finished read gaps 1126s Mutating sequence Sim.pm.2 1126s Introducing 9 SNPs, 2/4 ref/read gaps, and 0 rearrangements 1126s Finished SNPs 1126s Finished ref gaps 1126s Finished read gaps 1126s Mutated reference genome to subject genome 1126s SNPs introduced: 13 1126s Reference gaps introduced: 2 1126s Read gaps introduced: 4 1126s Rearrangements introduced: 1 1126s Created read sampler 1126s Sampling 6 reads 1126s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1126s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1126s parsing sequence Sim.pm.1... 1126s parsing sequence Sim.pm.2... 1126s Parsed 269 reference bases 1126s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1126s *** Run 13 of 100 1126s /usr/bin/bowtie2 -N 0 -L22 --score-min L,6.22242051544867,5.56370800915881 -i S,3.42540896924202 --cp-ival 1 --mm --cp-min 5 --large-index --mp 7.43676457280526,6.6171854680687 --trim3 0 -a --local --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1126s 6 reads; of these: 1126s 6 (100.00%) were unpaired; of these: 1126s 6 (100.00%) aligned 0 times 1126s 0 (0.00%) aligned exactly 1 time 1126s 0 (0.00%) aligned >1 times 1126s 0.00% overall alignment rate 1126s Processing line... 1126s Processing line... 1126s Processing line... 1126s Processing line... 1126s Processing line... 1126s Processing line... 1126s Processing line... 1126s Processing line... 1126s Processing line... 1126s Processing line... 1126s --- Summary --- 1126s Read 1 reference strings 1126s Checked 0 alignments, 0 edits 1126s --------------- 1126s PASSED 1126s ALSO checking that bowtie2 and bowtie2-align match up 1126s /usr/bin/bowtie2 -N 0 -L22 --score-min L,6.22242051544867,5.56370800915881 -i S,3.42540896924202 --cp-ival 1 --mm --cp-min 5 --large-index --mp 7.43676457280526,6.6171854680687 --trim3 0 -a --local --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1126s 6 reads; of these: 1126s 6 (100.00%) were unpaired; of these: 1126s 6 (100.00%) aligned 0 times 1126s 0 (0.00%) aligned exactly 1 time 1126s 0 (0.00%) aligned >1 times 1126s 0.00% overall alignment rate 1126s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1126s Flattened IUPAC characters 1126s Mutating sequence Sim.pm.1 1126s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1126s Finished SNPs 1126s Finished ref gaps 1126s Finished read gaps 1126s Mutating sequence Sim.pm.2 1126s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1126s Finished SNPs 1126s Finished ref gaps 1126s Finished read gaps 1126s Mutated reference genome to subject genome 1126s SNPs introduced: 11 1126s Reference gaps introduced: 1 1126s Read gaps introduced: 1 1126s Rearrangements introduced: 0 1126s Created read sampler 1126s Sampling 52 reads 1126s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1126s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1126s parsing sequence Sim.pm.1... 1126s parsing sequence Sim.pm.2... 1126s Parsed 269 reference bases 1126s *** Run 14 of 100 1126s /usr/bin/bowtie2 --rfg 29.9783007233197 --trim5 2 --score-min L,2.25672408045342,1.60787548621624 --n-ceil 0.188830467663049,0.744406042282709 --norc --nofw -D 15 --mp 4.64461296135192,3.6318507663474 --trim3 7 -k 4 --large-index --cp-min 7 --mm --cp-ival 1 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1127s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read '1' because it was < 2 characters long 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1127s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1127s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1127s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read '36' because it was < 2 characters long 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1127s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1127s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1127s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1127s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read '48' because it was < 2 characters long 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1127s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1127s 52 reads; of these: 1127s 41 (78.85%) were paired; of these: 1127s 41 (100.00%) aligned concordantly 0 times 1127s 0 (0.00%) aligned concordantly exactly 1 time 1127s 0 (0.00%) aligned concordantly >1 times 1127s ---- 1127s 41 pairs aligned concordantly 0 times; of these: 1127s 0 (0.00%) aligned discordantly 1 time 1127s ---- 1127s 41 pairs aligned 0 times concordantly or discordantly; of these: 1127s 82 mates make up the pairs; of these: 1127s 82 (100.00%) aligned 0 times 1127s 0 (0.00%) aligned exactly 1 time 1127s 0 (0.00%) aligned >1 times 1127s 11 (21.15%) were unpaired; of these: 1127s 11 (100.00%) aligned 0 times 1127s 0 (0.00%) aligned exactly 1 time 1127s 0 (0.00%) aligned >1 times 1127s 0.00% overall alignment rate 1127s Read 50 alignments... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s --- Summary --- 1127s Read 1 reference strings 1127s Checked 0 alignments, 0 edits 1127s --------------- 1127s PASSED 1127s Flattened IUPAC characters 1127s Mutating sequence Sim.pm.1 1127s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1127s Finished SNPs 1127s Finished ref gaps 1127s Finished read gaps 1127s Mutating sequence Sim.pm.2 1127s Introducing 23 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1127s Finished SNPs 1127s Finished ref gaps 1127s Finished read gaps 1127s Mutated reference genome to subject genome 1127s SNPs introduced: 27 1127s Reference gaps introduced: 0 1127s Read gaps introduced: 1 1127s Rearrangements introduced: 1 1127s Created read sampler 1127s Sampling 89 reads 1127s *** Run 15 of 100 1127s /usr/bin/bowtie2 --cp-ival 1 --cp-min 6 --large-index --local --rdg 31.3867457815788 --trim3 5 --nofw --gbar 7 --score-min L,9.2629905321422,7.71995989382108 -i S,2.78566851782698 --trim5 7 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq 1127s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1127s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1127s parsing sequence Sim.pm.1... 1127s parsing sequence Sim.pm.2... 1127s Parsed 269 reference bases 1127s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1127s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1127s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1127s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1127s Read 50 alignments... 1127s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 1127s Read 100 alignments... 1127s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 1127s 89 reads; of these: 1127s 71 (79.78%) were paired; of these: 1127s 71 (100.00%) aligned concordantly 0 times 1127s 0 (0.00%) aligned concordantly exactly 1 time 1127s 0 (0.00%) aligned concordantly >1 times 1127s ---- 1127s 71 pairs aligned concordantly 0 times; of these: 1127s 0 (0.00%) aligned discordantly 1 time 1127s ---- 1127s 71 pairs aligned 0 times concordantly or discordantly; of these: 1127s 142 mates make up the pairs; of these: 1127s 142 (100.00%) aligned 0 times 1127s 0 (0.00%) aligned exactly 1 time 1127s 0 (0.00%) aligned >1 times 1127s 18 (20.22%) were unpaired; of these: 1127s 18 (100.00%) aligned 0 times 1127s 0 (0.00%) aligned exactly 1 time 1127s 0 (0.00%) aligned >1 times 1127s 0.00% overall alignment rate 1127s Read 150 alignments... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s Processing line... 1127s --- Summary --- 1127s Read 1 reference strings 1127s Checked 0 alignments, 0 edits 1127s --------------- 1127s PASSED 1127s ALSO checking that bowtie2 and bowtie2-align match up 1127s /usr/bin/bowtie2 --cp-ival 1 --cp-min 6 --large-index --local --rdg 31.3867457815788 --trim3 5 --nofw --gbar 7 --score-min L,9.2629905321422,7.71995989382108 -i S,2.78566851782698 --trim5 7 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1127s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1127s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1127s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 1127s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1127s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 1127s 89 reads; of these: 1127s 71 (79.78%) were paired; of these: 1127s 71 (100.00%) aligned concordantly 0 times 1127s 0 (0.00%) aligned concordantly exactly 1 time 1127s 0 (0.00%) aligned concordantly >1 times 1127s ---- 1127s 71 pairs aligned concordantly 0 times; of these: 1127s 0 (0.00%) aligned discordantly 1 time 1127s ---- 1127s 71 pairs aligned 0 times concordantly or discordantly; of these: 1127s 142 mates make up the pairs; of these: 1127s 142 (100.00%) aligned 0 times 1127s 0 (0.00%) aligned exactly 1 time 1127s 0 (0.00%) aligned >1 times 1127s 18 (20.22%) were unpaired; of these: 1127s 18 (100.00%) aligned 0 times 1127s 0 (0.00%) aligned exactly 1 time 1127s 0 (0.00%) aligned >1 times 1127s 0.00% overall alignment rate 1127s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1127s Flattened IUPAC characters 1127s Mutating sequence Sim.pm.2 1127s Introducing 25 SNPs, 1/0 ref/read gaps, and 2 rearrangements 1127s Finished SNPs 1127s Finished ref gaps 1127s Finished read gaps 1127s Mutating sequence Sim.pm.1 1127s Introducing 1 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1127s Finished SNPs 1127s Finished ref gaps 1127s Finished read gaps 1127s Mutated reference genome to subject genome 1127s SNPs introduced: 26 1127s Reference gaps introduced: 1 1127s Read gaps introduced: 2 1127s Rearrangements introduced: 2 1127s Created read sampler 1127s Sampling 21 reads 1127s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1127s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1127s parsing sequence Sim.pm.1... 1127s parsing sequence Sim.pm.2... 1127s Parsed 269 reference bases 1127s *** Run 16 of 100 1127s /usr/bin/bowtie2 --np 3 --trim5 0 --rfg 6.57572458867756,11.1503082452231 --n-ceil 1.16991149887558,0.516829221244196 --score-min L,4.59829960011666,9.90616354673351 --cp-min 2 --mm --cp-ival 1 --mp 7.97209934872968,7.32654806122025 --trim3 9 --large-index --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1127s 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 1127s 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 1127s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1127s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1127s 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 1127s 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 1127s 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 1127s 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 1127s 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 1127s 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 1128s 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 1128s 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 1128s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1128s 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 1128s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1128s 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 1128s 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 1128s 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 1128s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1128s 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 1128s 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 1128s 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 1128s 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 1128s 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 1128s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 1128s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1128s 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 1128s 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 1128s 21 reads; of these: 1128s 21 (100.00%) were unpaired; of these: 1128s 16 (76.19%) aligned 0 times 1128s 3 (14.29%) aligned exactly 1 time 1128s 2 (9.52%) aligned >1 times 1128s 23.81% overall alignment rate 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s GAGCCTGTCA 1128s GAGCCTGTCA 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s AAATTA 1128s AAATTA 1128s Processing line... 1128s TGGATAACC 1128s TGGATAACC 1128s Processing line... 1128s AAATTA 1128s AAATTA 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s TGAGAC 1128s TGAGAC 1128s Processing line... 1128s --- Summary --- 1128s Read 1 reference strings 1128s Checked 5 alignments, 0 edits 1128s --------------- 1128s PASSED 1128s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1128s /usr/bin/bowtie2 --np 3 --trim5 0 --rfg 6.57572458867756,11.1503082452231 --n-ceil 1.16991149887558,0.516829221244196 --score-min L,4.59829960011666,9.90616354673351 --cp-min 2 --mm --cp-ival 1 --mp 7.97209934872968,7.32654806122025 --trim3 9 --large-index --qseq -p 2 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1128s 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 1128s 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 1128s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1128s 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 1128s 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 1128s 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 1128s 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 1128s 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 1128s 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 1128s 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 1128s 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 1128s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1128s 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 1128s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1128s 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 1128s 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 1128s 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 1128s 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 1128s 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 1128s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1128s 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 1128s 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 1128s 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 1128s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 1128s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1128s 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 1128s 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 1128s 21 reads; of these: 1128s 21 (100.00%) were unpaired; of these: 1128s 16 (76.19%) aligned 0 times 1128s 3 (14.29%) aligned exactly 1 time 1128s 2 (9.52%) aligned >1 times 1128s 23.81% overall alignment rate 1128s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1128s Flattened IUPAC characters 1128s Mutating sequence Sim.pm.1 1128s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1128s Finished SNPs 1128s Finished ref gaps 1128s Finished read gaps 1128s Mutating sequence Sim.pm.2 1128s Introducing 22 SNPs, 2/0 ref/read gaps, and 0 rearrangements 1128s Finished SNPs 1128s Finished ref gaps 1128s Finished read gaps 1128s Mutated reference genome to subject genome 1128s SNPs introduced: 24 1128s Reference gaps introduced: 2 1128s Read gaps introduced: 0 1128s Rearrangements introduced: 0 1128s Created read sampler 1128s Sampling 94 reads 1128s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1128s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1128s parsing sequence Sim.pm.1... 1128s parsing sequence Sim.pm.2... 1128s Parsed 269 reference bases 1128s *** Run 17 of 100 1128s /usr/bin/bowtie2 --score-min L,6.65451700363026,5.53069042978282 --n-ceil 1.17817584548376,0.643528448510877 --large-index -M 4 --rdg 13.9003281004391,18.4503906249456 --cp-ival 1 --np 3 --nofw --cp-min 2 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1128s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1128s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 1128s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1128s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 1128s Warning: skipping mate #1 of read '62' because it was < 2 characters long 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1128s Read 50 alignments... 1128s Read 100 alignments... 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1128s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 1128s Warning: skipping mate #2 of read '77' because it was < 2 characters long 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1128s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 1128s Warning: skipping mate #2 of read '85' because it was < 2 characters long 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1128s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1128s 94 reads; of these: 1128s 94 (100.00%) were paired; of these: 1128s 92 (97.87%) aligned concordantly 0 times 1128s 0 (0.00%) aligned concordantly exactly 1 time 1128s 2 (2.13%) aligned concordantly >1 times 1128s ---- 1128s 92 pairs aligned concordantly 0 times; of these: 1128s 0 (0.00%) aligned discordantly 1 time 1128s ---- 1128s 92 pairs aligned 0 times concordantly or discordantly; of these: 1128s 184 mates make up the pairs; of these: 1128s 167 (90.76%) aligned 0 times 1128s 2 (1.09%) aligned exactly 1 time 1128s 15 (8.15%) aligned >1 times 1128s 11.17% overall alignment rate 1128s Read 150 alignments... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s GC 1128s GC 1128s Processing line... 1128s CGAGCCTGT 1128s CGAGCCTGT 1128s Processing line... 1128s AGCCTGTCACATCGAGATGGACC 1128s AGCCTGTCACATCGAGATGGACC 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s ATCG 1128s ATCG 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s GTC 1128s GTC 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s GATAACCAAA 1128s GATAACCAAA 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s ACACGAGCCTGT 1128s ACACGAGCCTGT 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s GAGCCTGTCACATC 1128s GAGCCTGTCACATC 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s CCTCG 1128s CCTCG 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s GC 1128s GC 1128s Processing line... 1128s Processing line... 1128s TA 1128s TA 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s AGCCTGTCACATCGAGAT 1128s AGCCTGTCACATCGAGAT 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s CCTCGTG 1128s CCTCGTG 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s ACGAGCCTG 1128s ACGAGCCTG 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s CGT 1128s CGT 1128s Processing line... 1128s Processing line... 1128s AAC 1128s AAC 1128s Processing line... 1128s GAGCCTGTCACATCGAGA 1128s GAGCCTGTCACATCGAGA 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s CATCGAGATGGACCA 1128s CATCGAGATGGACCA 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s TGGTGAG 1128s TGGTGAG 1128s Processing line... 1128s Processing line... 1128s CGT 1128s CGT 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s Processing line... 1128s GGAC 1128s GGAC 1128s Processing line... 1128s --- Summary --- 1128s Read 1 reference strings 1128s Checked 21 alignments, 0 edits 1128s --------------- 1128s PASSED 1128s Flattened IUPAC characters 1128s Mutating sequence Sim.pm.2 1128s Introducing 17 SNPs, 2/1 ref/read gaps, and 3 rearrangements 1128s Finished SNPs 1128s Finished ref gaps 1128s Finished read gaps 1128s Mutating sequence Sim.pm.1 1128s Introducing 1 SNPs, 3/0 ref/read gaps, and 1 rearrangements 1128s Finished SNPs 1128s Finished ref gaps 1128s Finished read gaps 1128s Mutated reference genome to subject genome 1128s SNPs introduced: 18 1128s Reference gaps introduced: 5 1128s Read gaps introduced: 1 1128s Rearrangements introduced: 4 1128s Created read sampler 1128s Sampling 87 reads 1128s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1128s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1128s parsing sequence Sim.pm.1... 1128s parsing sequence Sim.pm.2... 1128s Parsed 269 reference bases 1128s *** Run 18 of 100 1128s /usr/bin/bowtie2 --large-index --local --mp 8.11175942956449,3.71651371237993 --cp-ival 1 --cp-min 3 --score-min L,9.28428393656581,9.12522805139627 --trim5 8 --nofw --np 3 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1128s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '3' because it was < 2 characters long 1128s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '4' because it was < 2 characters long 1128s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '5' because it was < 2 characters long 1128s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '6' because it was < 2 characters long 1128s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1128s Warning: skipping read '7' because it was < 2 characters long 1128s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '12' because it was < 2 characters long 1128s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '18' because it was < 2 characters long 1128s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '27' because it was < 2 characters long 1128s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '42' because it was < 2 characters long 1128s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '49' because it was < 2 characters long 1128s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '54' because it was < 2 characters long 1128s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '61' because it was < 2 characters long 1128s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '66' because it was < 2 characters long 1128s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '69' because it was < 2 characters long 1128s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '70' because it was < 2 characters long 1128s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '73' because it was < 2 characters long 1128s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '75' because it was < 2 characters long 1128s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 1128s Warning: skipping read '76' because it was < 2 characters long 1128s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 1128s Warning: skipping read '77' because it was < 2 characters long 1128s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '78' because it was < 2 characters long 1128s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '86' because it was < 2 characters long 1128s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1128s Warning: skipping read '87' because it was < 2 characters long 1128s 87 reads; of these: 1128s 87 (100.00%) were unpaired; of these: 1128s 87 (100.00%) aligned 0 times 1128s 0 (0.00%) aligned exactly 1 time 1128s 0 (0.00%) aligned >1 times 1128s 0.00% overall alignment rate 1128s Read 50 alignments... 1128s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s /usr/bin/bowtie2 --large-index --local --mp 8.11175942956449,3.71651371237993 --cp-ival 1 --cp-min 3 --score-min L,9.28428393656581,9.12522805139627 --trim5 8 --nofw --np 3 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1129s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1129s /usr/bin/bowtie2 --large-index --local --mp 8.11175942956449,3.71651371237993 --cp-ival 1 --cp-min 3 --score-min L,9.28428393656581,9.12522805139627 --trim5 8 --nofw --np 3 -q -p 4 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s Processing line... 1129s --- Summary --- 1129s Read 1 reference strings 1129s Checked 0 alignments, 0 edits 1129s --------------- 1129s PASSED 1129s ALSO checking that bowtie2 and bowtie2-align match up 1129s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '3' because it was < 2 characters long 1129s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '4' because it was < 2 characters long 1129s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '5' because it was < 2 characters long 1129s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '6' because it was < 2 characters long 1129s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1129s Warning: skipping read '7' because it was < 2 characters long 1129s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '12' because it was < 2 characters long 1129s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '18' because it was < 2 characters long 1129s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '27' because it was < 2 characters long 1129s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '42' because it was < 2 characters long 1129s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '49' because it was < 2 characters long 1129s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '54' because it was < 2 characters long 1129s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '61' because it was < 2 characters long 1129s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '66' because it was < 2 characters long 1129s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '69' because it was < 2 characters long 1129s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '70' because it was < 2 characters long 1129s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '73' because it was < 2 characters long 1129s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '75' because it was < 2 characters long 1129s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 1129s Warning: skipping read '76' because it was < 2 characters long 1129s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 1129s Warning: skipping read '77' because it was < 2 characters long 1129s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '78' because it was < 2 characters long 1129s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '86' because it was < 2 characters long 1129s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1129s Warning: skipping read '87' because it was < 2 characters long 1129s 87 reads; of these: 1129s 87 (100.00%) were unpaired; of these: 1129s 87 (100.00%) aligned 0 times 1129s 0 (0.00%) aligned exactly 1 time 1129s 0 (0.00%) aligned >1 times 1129s 0.00% overall alignment rate 1129s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1131s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '3' because it was < 2 characters long 1131s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '4' because it was < 2 characters long 1131s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '5' because it was < 2 characters long 1131s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '6' because it was < 2 characters long 1131s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1131s Warning: skipping read '7' because it was < 2 characters long 1131s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '12' because it was < 2 characters long 1131s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '18' because it was < 2 characters long 1131s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '27' because it was < 2 characters long 1131s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1131s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '42' because it was < 2 characters long 1131s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '66' because it was < 2 characters long 1131s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '69' because it was < 2 characters long 1131s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '70' because it was < 2 characters long 1131s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '73' because it was < 2 characters long 1131s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '75' because it was < 2 characters long 1131s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 1131s Warning: skipping read '76' because it was < 2 characters long 1131s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 1131s Warning: skipping read '77' because it was < 2 characters long 1131s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '78' because it was < 2 characters long 1131s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '86' because it was < 2 characters long 1131s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '87' because it was < 2 characters long 1131s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '49' because it was < 2 characters long 1131s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '54' because it was < 2 characters long 1131s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '61' because it was < 2 characters long 1131s 87 reads; of these: 1131s 87 (100.00%) were unpaired; of these: 1131s 87 (100.00%) aligned 0 times 1131s 0 (0.00%) aligned exactly 1 time 1131s 0 (0.00%) aligned >1 times 1131s 0.00% overall alignment rate 1131s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1131s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '3' because it was < 2 characters long 1131s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '4' because it was < 2 characters long 1131s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '5' because it was < 2 characters long 1131s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '6' because it was < 2 characters long 1131s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1131s Warning: skipping read '7' because it was < 2 characters long 1131s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '12' because it was < 2 characters long 1131s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '18' because it was < 2 characters long 1131s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '27' because it was < 2 characters long 1131s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '42' because it was < 2 characters long 1131s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '49' because it was < 2 characters long 1131s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '54' because it was < 2 characters long 1131s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '61' because it was < 2 characters long 1131s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '66' because it was < 2 characters long 1131s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '69' because it was < 2 characters long 1131s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '70' because it was < 2 characters long 1131s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '86' because it was < 2 characters long 1131s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '87' because it was < 2 characters long 1131s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '73' because it was < 2 characters long 1131s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '75' because it was < 2 characters long 1131s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 1131s Warning: skipping read '76' because it was < 2 characters long 1131s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 1131s Warning: skipping read '77' because it was < 2 characters long 1131s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1131s Warning: skipping read '78' because it was < 2 characters long 1131s 87 reads; of these: 1131s 87 (100.00%) were unpaired; of these: 1131s 87 (100.00%) aligned 0 times 1131s 0 (0.00%) aligned exactly 1 time 1131s 0 (0.00%) aligned >1 times 1131s 0.00% overall alignment rate 1131s Flattened IUPAC characters 1131s Mutating sequence Sim.pm.2 1131s Introducing 8 SNPs, 5/1 ref/read gaps, and 3 rearrangements 1131s Finished SNPs 1131s Finished ref gaps 1131s Finished read gaps 1131s Mutating sequence Sim.pm.1 1131s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1131s Finished SNPs 1131s Finished ref gaps 1131s Finished read gaps 1131s Mutated reference genome to subject genome 1131s SNPs introduced: 9 1131s Reference gaps introduced: 5 1131s Read gaps introduced: 1 1131s Rearrangements introduced: 4 1131s Created read sampler 1131s Sampling 149 reads 1131s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1131s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1131s parsing sequence Sim.pm.1... 1131s parsing sequence Sim.pm.2... 1131s Parsed 269 reference bases 1131s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 1131s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1131s Read 50 alignments... 1131s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 1131s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1131s Read 100 alignments... 1131s Read 150 alignments... 1131s 149 reads; of these: 1131s 149 (100.00%) were paired; of these: 1131s 149 (100.00%) aligned concordantly 0 times 1131s 0 (0.00%) aligned concordantly exactly 1 time 1131s 0 (0.00%) aligned concordantly >1 times 1131s ---- 1131s 149 pairs aligned concordantly 0 times; of these: 1131s 0 (0.00%) aligned discordantly 1 time 1131s ---- 1131s 149 pairs aligned 0 times concordantly or discordantly; of these: 1131s 298 mates make up the pairs; of these: 1131s 298 (100.00%) aligned 0 times 1131s 0 (0.00%) aligned exactly 1 time 1131s 0 (0.00%) aligned >1 times 1131s 0.00% overall alignment rate 1131s Read 200 alignments... 1131s Read 250 alignments... 1131s Read 300 alignments... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s 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Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s --- Summary --- 1131s Read 1 reference strings 1131s Checked 0 alignments, 0 edits 1131s --------------- 1131s PASSED 1131s ALSO checking that bowtie2 and bowtie2-align match up 1131s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 1131s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1131s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 1131s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1131s 149 reads; of these: 1131s 149 (100.00%) were paired; of these: 1131s 149 (100.00%) aligned concordantly 0 times 1131s 0 (0.00%) aligned concordantly exactly 1 time 1131s 0 (0.00%) aligned concordantly >1 times 1131s ---- 1131s 149 pairs aligned concordantly 0 times; of these: 1131s 0 (0.00%) aligned discordantly 1 time 1131s ---- 1131s 149 pairs aligned 0 times concordantly or discordantly; of these: 1131s 298 mates make up the pairs; of these: 1131s 298 (100.00%) aligned 0 times 1131s 0 (0.00%) aligned exactly 1 time 1131s 0 (0.00%) aligned >1 times 1131s 0.00% overall alignment rate 1131s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1131s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 1131s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1131s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 1131s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1131s 149 reads; of these: 1131s 149 (100.00%) were paired; of these: 1131s 149 (100.00%) aligned concordantly 0 times 1131s 0 (0.00%) aligned concordantly exactly 1 time 1131s 0 (0.00%) aligned concordantly >1 times 1131s ---- 1131s 149 pairs aligned concordantly 0 times; of these: 1131s 0 (0.00%) aligned discordantly 1 time 1131s ---- 1131s 149 pairs aligned 0 times concordantly or discordantly; of these: 1131s 298 mates make up the pairs; of these: 1131s 298 (100.00%) aligned 0 times 1131s 0 (0.00%) aligned exactly 1 time 1131s 0 (0.00%) aligned >1 times 1131s 0.00% overall alignment rate 1131s Flattened IUPAC characters 1131s Mutating sequence Sim.pm.1 1131s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1131s Finished SNPs 1131s Finished ref gaps 1131s Finished read gaps 1131s Mutating sequence Sim.pm.2 1131s Introducing 11 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1131s Finished SNPs 1131s Finished ref gaps 1131s Finished read gaps 1131s Mutated reference genome to subject genome 1131s SNPs introduced: 11 1131s Reference gaps introduced: 0 1131s Read gaps introduced: 0 1131s Rearrangements introduced: 0 1131s Created read sampler 1131s Sampling 103 reads 1131s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1131s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1131s parsing sequence Sim.pm.1... 1131s parsing sequence Sim.pm.2... 1131s Parsed 269 reference bases 1131s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1131s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '1' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1131s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '13' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1131s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '34' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1131s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '36' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1131s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '51' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1131s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '59' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1131s Warning: skipping read '64' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '64' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1131s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '68' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1131s Warning: skipping read '74' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '74' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1131s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '80' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1131s Warning: skipping read '84' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '84' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1131s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '91' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1131s Warning: skipping read '92' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '92' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1131s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '100' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1131s 103 reads; of these: 1131s 103 (100.00%) were unpaired; of these: 1131s 103 (100.00%) aligned 0 times 1131s 0 (0.00%) aligned exactly 1 time 1131s 0 (0.00%) aligned >1 times 1131s 0.00% overall alignment rate 1131s Read 50 alignments... 1131s Read 100 alignments... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s --- Summary --- 1131s Read 1 reference strings 1131s Checked 0 alignments, 0 edits 1131s --------------- 1131s PASSED 1131s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1131s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1131s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '1' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1131s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '13' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1131s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '34' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1131s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '36' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1131s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '51' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1131s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '68' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1131s Warning: skipping read '74' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '74' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1131s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '80' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1131s Warning: skipping read '84' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '84' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1131s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '91' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1131s Warning: skipping read '92' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '92' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1131s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '59' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1131s Warning: skipping read '64' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '64' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1131s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 1131s Warning: skipping read '100' because it was < 2 characters long 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1131s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1131s 103 reads; of these: 1131s 103 (100.00%) were unpaired; of these: 1131s 103 (100.00%) aligned 0 times 1131s 0 (0.00%) aligned exactly 1 time 1131s 0 (0.00%) aligned >1 times 1131s 0.00% overall alignment rate 1131s Flattened IUPAC characters 1131s Mutating sequence Sim.pm.2 1131s Introducing 2 SNPs, 3/0 ref/read gaps, and 1 rearrangements 1131s Finished SNPs 1131s Finished ref gaps 1131s Finished read gaps 1131s Mutating sequence Sim.pm.1 1131s Introducing 10 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1131s Finished SNPs 1131s Finished ref gaps 1131s Finished read gaps 1131s Mutated reference genome to subject genome 1131s SNPs introduced: 12 1131s Reference gaps introduced: 3 1131s Read gaps introduced: 1 1131s Rearrangements introduced: 1 1131s Created read sampler 1131s Sampling 36 reads 1131s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1131s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1131s parsing sequence Sim.pm.1... 1131s parsing sequence Sim.pm.2... 1131s Parsed 269 reference bases 1131s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1131s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1131s /usr/bin/bowtie2 --large-index --local --mp 8.11175942956449,3.71651371237993 --cp-ival 1 --cp-min 3 --score-min L,9.28428393656581,9.12522805139627 --trim5 8 --nofw --np 3 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1131s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1131s *** Run 19 of 100 1131s /usr/bin/bowtie2 --n-ceil 0.729600181577735,0.120696044414846 --score-min L,3.42033482702843,5.22482814505249 --np 1 --trim3 0 --local --large-index --cp-min 11 --cp-ival 1 --mm -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1131s /usr/bin/bowtie2 --n-ceil 0.729600181577735,0.120696044414846 --score-min L,3.42033482702843,5.22482814505249 --np 1 --trim3 0 --local --large-index --cp-min 11 --cp-ival 1 --mm -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1131s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1131s /usr/bin/bowtie2 --n-ceil 0.729600181577735,0.120696044414846 --score-min L,3.42033482702843,5.22482814505249 --np 1 --trim3 0 --local --large-index --cp-min 11 --cp-ival 1 --mm -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1131s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1131s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1131s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1131s *** Run 20 of 100 1131s /usr/bin/bowtie2 --cp-min 3 --mm --cp-ival 2 --rdg 22.4482285422736 --trim3 0 --large-index --ma 16.9736247811271 -k 2 --norc --np 4 --nofw -N 1 -D 45 --trim5 5 --rfg 18.1627607004878 --score-min L,2.55415690695091,6.63598588484284 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1131s /usr/bin/bowtie2 --cp-min 3 --mm --cp-ival 2 --rdg 22.4482285422736 --trim3 0 --large-index --ma 16.9736247811271 -k 2 --norc --np 4 --nofw -N 1 -D 45 --trim5 5 --rfg 18.1627607004878 --score-min L,2.55415690695091,6.63598588484284 -f -p 2 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1131s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1131s *** Run 21 of 100 1131s /usr/bin/bowtie2 --large-index --rdg 43.7181325694738 --trim3 0 --mp 9.60763244361093,5.151620306488 --local --mm --cp-ival 1 --cp-min 3 --n-ceil 1.20512543871797,0.451056657051582 --score-min L,8.29315055623548,1.20776710783141 --rfg 20.7382846897255,6.59496864796259 -R 1 --norc --np 5 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq 1131s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 1131s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1131s 36 reads; of these: 1131s 36 (100.00%) were paired; of these: 1131s 33 (91.67%) aligned concordantly 0 times 1131s 2 (5.56%) aligned concordantly exactly 1 time 1131s 1 (2.78%) aligned concordantly >1 times 1131s ---- 1131s 33 pairs aligned concordantly 0 times; of these: 1131s 0 (0.00%) aligned discordantly 1 time 1131s ---- 1131s 33 pairs aligned 0 times concordantly or discordantly; of these: 1131s 66 mates make up the pairs; of these: 1131s 62 (93.94%) aligned 0 times 1131s 1 (1.52%) aligned exactly 1 time 1131s 3 (4.55%) aligned >1 times 1131s 13.89% overall alignment rate 1131s Read 50 alignments... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s GGATAACCAAAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGCTGGATAACCAGAGTAGAACACGAGCCTGTCAGTCA 1131s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCA--CA 1131s Processing line... 1131s GGATAACCAAAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGCTGGATAACCAGAGTAGAACACGAGCCTGTCAGTCA 1131s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCA--CA 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s GGATAACCACAGTAGAACACGGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATAACCATAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1131s GGATAACCANAGTAGAACAC-GAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s GGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCACAGTAGAACACGGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATAACC 1131s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACAC-GAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACC 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s TGGATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGCTGGATAACCAGAGTAGAACACGAGCCTGTCAGTCATCGAGATGGACCACCTCGTGGGTTGGATAACCAAAACGCGGAAATTAGAGCTCGCAGCGGGTAAAAGGGTGGGGTATGGTGAGGGTCGAGG 1131s TGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCA--CATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAACGCNGAAATTAGAGCTCGCAGCGCGTAANAGGGNGGGGTATGGTGAGGGTCGA-G 1131s Processing line... 1131s Processing line... 1131s ATGGACCACCTCGTGGGGTGGATAACCACAGTAGAACACGGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATAACCATAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGATAACCAAAACGCTGAA 1131s ATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACAC-GAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAACGCNG-A 1131s Processing line... 1131s GTGGGATGGATAACCAAAACGCTGAAATTAG 1131s GTGGGNTGGATAACCAAAACGCNGAAATTAG 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s ATCGAGATGGAC 1131s ATCGAGATGGAC 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s Processing line... 1131s GGATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGCTGGATAACCAGAGTAGAACACGAGCCTGTCAGTCATCGAGATGGACCACCTCGTGGGTTGGATAACCAAAACGCGGAAATTAGAGCTCGCAGCGGGTAAAAGGG 1131s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCA--CATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAACGCNGAAATTAGAGCTCGCAGCGCGTAANAGGG 1131s Processing line... 1131s GGGGTATGGTGAGGGTCGAGGA 1131s GGGGTATGGTGAGGGTCGAGGA 1131s --- Summary --- 1131s Read 1 reference strings 1131s Checked 10 alignments, 0 edits 1131s /usr/bin/bowtie2 --large-index --rdg 43.7181325694738 --trim3 0 --mp 9.60763244361093,5.151620306488 --local --mm --cp-ival 1 --cp-min 3 --n-ceil 1.20512543871797,0.451056657051582 --score-min L,8.29315055623548,1.20776710783141 --rfg 20.7382846897255,6.59496864796259 -R 1 --norc --np 5 --qseq -p 3 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1131s --------------- 1131s PASSED 1131s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1131s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 1131s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1131s 36 reads; of these: 1131s 36 (100.00%) were paired; of these: 1131s 33 (91.67%) aligned concordantly 0 times 1131s 2 (5.56%) aligned concordantly exactly 1 time 1131s 1 (2.78%) aligned concordantly >1 times 1131s ---- 1131s 33 pairs aligned concordantly 0 times; of these: 1131s 0 (0.00%) aligned discordantly 1 time 1131s ---- 1131s 33 pairs aligned 0 times concordantly or discordantly; of these: 1131s 66 mates make up the pairs; of these: 1131s 62 (93.94%) aligned 0 times 1131s 1 (1.52%) aligned exactly 1 time 1131s 3 (4.55%) aligned >1 times 1131s 13.89% overall alignment rate 1131s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1131s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1131s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1131s Flattened IUPAC characters 1131s Mutating sequence Sim.pm.2 1131s Introducing 6 SNPs, 5/3 ref/read gaps, and 1 rearrangements 1131s Finished SNPs 1131s Finished ref gaps 1131s Finished read gaps 1131s Mutating sequence Sim.pm.1 1131s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1131s Finished SNPs 1131s Finished ref gaps 1131s Finished read gaps 1131s Mutated reference genome to subject genome 1131s SNPs introduced: 8 1131s Reference gaps introduced: 5 1131s Read gaps introduced: 3 1131s Rearrangements introduced: 2 1131s Created read sampler 1131s Sampling 56 reads 1131s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1131s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1131s parsing sequence Sim.pm.1... 1131s parsing sequence Sim.pm.2... 1131s Parsed 269 reference bases 1131s *** Run 22 of 100 1131s /usr/bin/bowtie2 --score-min L,5.62719329647321,8.17340151953471 --trim5 2 --ma 2.88532849459579 --large-index -M 3 --mp 7.93115181389633,2.82704713023221 --cp-ival 1 --cp-min 3 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq 1131s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1131s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s Warning: skipping mate #2 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 1131s Warning: skipping mate #2 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1131s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s 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 1132s Read 50 alignments... 1132s 56 reads; of these: 1132s 54 (96.43%) were paired; of these: 1132s 52 (96.30%) aligned concordantly 0 times 1132s 0 (0.00%) aligned concordantly exactly 1 time 1132s 2 (3.70%) aligned concordantly >1 times 1132s ---- 1132s 52 pairs aligned concordantly 0 times; of these: 1132s 1 (1.92%) aligned discordantly 1 time 1132s ---- 1132s 51 pairs aligned 0 times concordantly or discordantly; of these: 1132s 102 mates make up the pairs; of these: 1132s 82 (80.39%) aligned 0 times 1132s 7 (6.86%) aligned exactly 1 time 1132s 13 (12.75%) aligned >1 times 1132s 2 (3.57%) were unpaired; of these: 1132s 2 (100.00%) aligned 0 times 1132s 0 (0.00%) aligned exactly 1 time 1132s 0 (0.00%) aligned >1 times 1132s 23.64% overall alignment rate 1132s Read 100 alignments... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s GG 1132s GG 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s TGTCACATCGAG 1132s TGTCACATCGAG 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s GTCACATCGAGATGGACCA 1132s GTCACATCGAGATGGACCA 1132s Processing line... 1132s Processing line... 1132s ACATCGAGATGGACCACCTCGTGG 1132s ACATCGAGATGGACCACCTCGTGG 1132s Processing line... 1132s Processing line... 1132s ACCAAA 1132s ACCAAA 1132s Processing line... 1132s Processing line... 1132s GAGATGG 1132s GAGATGG 1132s Processing line... 1132s ACGAGCCTGTCACAT 1132s ACGAGCCTGTCACAT 1132s Processing line... 1132s Processing line... 1132s AGGGTCGAGGAC 1132s AGGGTCGAGGAC 1132s Processing line... 1132s Processing line... 1132s GA 1132s GA 1132s Processing line... 1132s Processing line... 1132s AG 1132s AG 1132s Processing line... 1132s TGG 1132s TGG 1132s Processing line... 1132s CTCGC 1132s CTCGC 1132s Processing line... 1132s CACG 1132s CACG 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s GAGCCTGTCA 1132s GAGCCTGTCA 1132s Processing line... 1132s Processing line... 1132s GAAA 1132s GAAA 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s CCTGTCACATCGAGATGGACCACCTCGTGG 1132s CCTGTCACATCGAGATGGACCACCTCGTGG 1132s Processing line... 1132s Processing line... 1132s ATCGAGATGGAC 1132s ATCGAGATGGAC 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s GAGGGTCGAG 1132s GAGGGTCGAG 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s AGATGGACCACC 1132s AGATGGACCACC 1132s Processing line... 1132s Processing line... 1132s GGACC 1132s GGACC 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s GTGAGGGTCGAG 1132s GTGAGGGTCGAG 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s TCGAGATGGACCACCT 1132s TCGAGATGGACCACCT 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s CC 1132s CC 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s GAGCTCGCAGCGCG 1132s GAGCTCGCAGCGCG 1132s Processing line... 1132s GGTATGGTGAGGGTCGAGG 1132s GGTATGGTGAGGGTCGAGG 1132s Processing line... 1132s GGTGAGGGTCGA 1132s GGTGAGGGTCGA 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s --- Summary --- 1132s Read 1 reference strings 1132s Checked 26 alignments, 0 edits 1132s --------------- 1132s PASSED 1132s Flattened IUPAC characters 1132s Mutating sequence Sim.pm.1 1132s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1132s Finished SNPs 1132s Finished ref gaps 1132s Finished read gaps 1132s Mutating sequence Sim.pm.2 1132s Introducing 1 SNPs, 3/2 ref/read gaps, and 1 rearrangements 1132s Finished SNPs 1132s Finished ref gaps 1132s Finished read gaps 1132s Mutated reference genome to subject genome 1132s SNPs introduced: 5 1132s Reference gaps introduced: 3 1132s Read gaps introduced: 2 1132s Rearrangements introduced: 1 1132s Created read sampler 1132s Sampling 137 reads 1132s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1132s *** Run 23 of 100 1132s /usr/bin/bowtie2 --rfg 10.1804912678626,5.38078648660651 --score-min L,6.82955529285232,2.14386128458577 --norc --nofw --np 13 --local --rdg 48.7966136050933,12.9809051041384 --mp 3.20052941145608,2.69436550374193 --trim3 8 --large-index --cp-min 4 --cp-ival 1 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1132s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1132s parsing sequence Sim.pm.1... 1132s parsing sequence Sim.pm.2... 1132s Parsed 269 reference bases 1132s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '6' because it was < 2 characters long 1132s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '11' because it was < 2 characters long 1132s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '12' because it was < 2 characters long 1132s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '13' because it was < 2 characters long 1132s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '17' because it was < 2 characters long 1132s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '21' because it was < 2 characters long 1132s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1132s Warning: skipping read '22' because it was < 2 characters long 1132s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '23' because it was < 2 characters long 1132s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 1132s Warning: skipping read '30' because it was < 2 characters long 1132s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '37' because it was < 2 characters long 1132s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '42' because it was < 2 characters long 1132s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '43' because it was < 2 characters long 1132s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '47' because it was < 2 characters long 1132s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '49' because it was < 2 characters long 1132s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '52' because it was < 2 characters long 1132s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '53' because it was < 2 characters long 1132s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '54' because it was < 2 characters long 1132s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '56' because it was < 2 characters long 1132s Warning: skipping read '61' because length (1) <= # seed mismatches (0) 1132s Warning: skipping read '61' because it was < 2 characters long 1132s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '63' because it was < 2 characters long 1132s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '65' because it was < 2 characters long 1132s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '67' because it was < 2 characters long 1132s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '69' because it was < 2 characters long 1132s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '73' because it was < 2 characters long 1132s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '79' because it was < 2 characters long 1132s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '84' because it was < 2 characters long 1132s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '89' because it was < 2 characters long 1132s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '92' because it was < 2 characters long 1132s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '95' because it was < 2 characters long 1132s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '98' because it was < 2 characters long 1132s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '107' because it was < 2 characters long 1132s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '111' because it was < 2 characters long 1132s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '112' because it was < 2 characters long 1132s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '121' because it was < 2 characters long 1132s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '125' because it was < 2 characters long 1132s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '127' because it was < 2 characters long 1132s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '131' because it was < 2 characters long 1132s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 1132s Warning: skipping read '134' because it was < 2 characters long 1132s Warning: skipping read '137' because length (1) <= # seed mismatches (0) 1132s Warning: skipping read '137' because it was < 2 characters long 1132s Read 50 alignments... 1132s Read 100 alignments... 1132s 137 reads; of these: 1132s 137 (100.00%) were unpaired; of these: 1132s 137 (100.00%) aligned 0 times 1132s 0 (0.00%) aligned exactly 1 time 1132s 0 (0.00%) aligned >1 times 1132s 0.00% overall alignment rate 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s --- Summary --- 1132s Read 1 reference strings 1132s Checked 0 alignments, 0 edits 1132s --------------- 1132s PASSED 1132s Flattened IUPAC characters 1132s Mutating sequence Sim.pm.2 1132s Introducing 15 SNPs, 1/1 ref/read gaps, and 1 rearrangements 1132s Finished SNPs 1132s Finished ref gaps 1132s Finished read gaps 1132s Mutating sequence Sim.pm.1 1132s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1132s Finished SNPs 1132s Finished ref gaps 1132s Finished read gaps 1132s Mutated reference genome to subject genome 1132s SNPs introduced: 18 1132s Reference gaps introduced: 1 1132s Read gaps introduced: 1 1132s Rearrangements introduced: 1 1132s Created read sampler 1132s Sampling 37 reads 1132s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1132s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1132s parsing sequence Sim.pm.1... 1132s parsing sequence Sim.pm.2... 1132s Parsed 269 reference bases 1132s *** Run 24 of 100 1132s /usr/bin/bowtie2 --cp-ival 1 --norc --nofw --cp-min 2 --score-min L,4.86027102783464,4.14831828400821 --large-index --n-ceil 0.281088181022785,0.133516028220236 --rfg 23.7073182212757,1.61587053693319 --mp 6.95604456181814,5.24065068944139 --trim3 4 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1132s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 1132s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1132s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 1132s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1132s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1132s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1132s 37 reads; of these: 1132s 33 (89.19%) were paired; of these: 1132s 33 (100.00%) aligned concordantly 0 times 1132s 0 (0.00%) aligned concordantly exactly 1 time 1132s 0 (0.00%) aligned concordantly >1 times 1132s ---- 1132s 33 pairs aligned concordantly 0 times; of these: 1132s 0 (0.00%) aligned discordantly 1 time 1132s ---- 1132s 33 pairs aligned 0 times concordantly or discordantly; of these: 1132s 66 mates make up the pairs; of these: 1132s 66 (100.00%) aligned 0 times 1132s 0 (0.00%) aligned exactly 1 time 1132s 0 (0.00%) aligned >1 times 1132s 4 (10.81%) were unpaired; of these: 1132s 4 (100.00%) aligned 0 times 1132s 0 (0.00%) aligned exactly 1 time 1132s 0 (0.00%) aligned >1 times 1132s 0.00% overall alignment rate 1132s Read 50 alignments... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s /usr/bin/bowtie2 --cp-ival 1 --norc --nofw --cp-min 2 --score-min L,4.86027102783464,4.14831828400821 --large-index --n-ceil 0.281088181022785,0.133516028220236 --rfg 23.7073182212757,1.61587053693319 --mp 6.95604456181814,5.24065068944139 --trim3 4 -q -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s Processing line... 1132s --- Summary --- 1132s Read 1 reference strings 1132s Checked 0 alignments, 0 edits 1132s --------------- 1132s PASSED 1132s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1132s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 1132s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1132s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 1132s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1132s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1132s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1132s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1132s 37 reads; of these: 1132s 33 (89.19%) were paired; of these: 1132s 33 (100.00%) aligned concordantly 0 times 1132s 0 (0.00%) aligned concordantly exactly 1 time 1132s 0 (0.00%) aligned concordantly >1 times 1132s ---- 1132s 33 pairs aligned concordantly 0 times; of these: 1132s 0 (0.00%) aligned discordantly 1 time 1132s ---- 1132s 33 pairs aligned 0 times concordantly or discordantly; of these: 1132s 66 mates make up the pairs; of these: 1132s 66 (100.00%) aligned 0 times 1132s 0 (0.00%) aligned exactly 1 time 1132s 0 (0.00%) aligned >1 times 1132s 4 (10.81%) were unpaired; of these: 1132s 4 (100.00%) aligned 0 times 1132s 0 (0.00%) aligned exactly 1 time 1132s 0 (0.00%) aligned >1 times 1132s 0.00% overall alignment rate 1132s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1133s Flattened IUPAC characters 1133s Mutating sequence Sim.pm.1 1133s Introducing 1 SNPs, 2/0 ref/read gaps, and 2 rearrangements 1133s Finished SNPs 1133s Finished ref gaps 1133s Finished read gaps 1133s Mutating sequence Sim.pm.2 1133s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1133s Finished SNPs 1133s Finished ref gaps 1133s Finished read gaps 1133s Mutated reference genome to subject genome 1133s SNPs introduced: 8 1133s Reference gaps introduced: 2 1133s Read gaps introduced: 0 1133s Rearrangements introduced: 3 1133s Created read sampler 1133s Sampling 30 reads 1133s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1133s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1133s *** Run 25 of 100 1133s /usr/bin/bowtie2 --np 1 --nofw -D 25 -R 4 -N 1 -L22 --rfg 26.4481187300245 --trim5 9 --score-min L,3.91684188085215,5.8604392074688 --cp-min 3 --cp-ival 1 --rdg 9.85136600507708,14.2495042040049 -a --trim3 2 --ma 35.617369123025 --large-index -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1133s parsing sequence Sim.pm.1... 1133s parsing sequence Sim.pm.2... 1133s Parsed 269 reference bases 1133s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1133s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 1133s Warning: skipping read '2' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1133s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (1) 1133s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1133s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 1133s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1133s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (1) 1133s Warning: skipping mate #1 of read '11' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1133s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (1) 1133s Warning: skipping mate #2 of read '23' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1133s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 1133s Warning: skipping read '24' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1133s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 1133s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1133s 30 reads; of these: 1133s 25 (83.33%) were paired; of these: 1133s 25 (100.00%) aligned concordantly 0 times 1133s 0 (0.00%) aligned concordantly exactly 1 time 1133s 0 (0.00%) aligned concordantly >1 times 1133s ---- 1133s 25 pairs aligned concordantly 0 times; of these: 1133s 0 (0.00%) aligned discordantly 1 time 1133s ---- 1133s 25 pairs aligned 0 times concordantly or discordantly; of these: 1133s 50 mates make up the pairs; of these: 1133s 42 (84.00%) aligned 0 times 1133s 0 (0.00%) aligned exactly 1 time 1133s 8 (16.00%) aligned >1 times 1133s 5 (16.67%) were unpaired; of these: 1133s 5 (100.00%) aligned 0 times 1133s 0 (0.00%) aligned exactly 1 time 1133s 0 (0.00%) aligned >1 times 1133s 14.55% overall alignment rate 1133s Read 50 alignments... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s GTCACATCG 1133s GTCACATCG 1133s Processing line... 1133s GTCACATCG 1133s GTCACATCG 1133s Processing line... 1133s GTCACATCG 1133s GTCACATCG 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s CTCG 1133s CTCG 1133s Processing line... 1133s CTCG 1133s CTCG 1133s Processing line... 1133s CTCG 1133s CTCG 1133s Processing line... 1133s CTCG 1133s CTCG 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s AT 1133s AT 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s GAACAC 1133s GAACAC 1133s Processing line... 1133s GAACAC 1133s GAACAC 1133s Processing line... 1133s GAACAC 1133s GAACAC 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s CCACCT 1133s CCACCT 1133s Processing line... 1133s CCACCT 1133s CCACCT 1133s Processing line... 1133s CCACCT 1133s CCACCT 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s GATGGACCACCTCGTGGG 1133s GATGGACCACCTCGTGGG 1133s Processing line... 1133s GATGGACCACCTCGTGGG 1133s GATGGACCACCTCGTGGG 1133s Processing line... 1133s GATGGACCACCTCGTGGG 1133s GATGGACCACCTCGTGGG 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s TAGAACACGAGCCTGTCACATCGAGA 1133s TAGAACACGAGCCTGTCACATCGAGA 1133s Processing line... 1133s TAGAACACGAGCCTGTCACATCGAGA 1133s TAGAACACGAGCCTGTCACATCGAGA 1133s Processing line... 1133s TAGAACACGAGCCTGTCACATCGAGA 1133s TAGAACACGAGCCTGTCACATCGAGA 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s CAC 1133s CAC 1133s Processing line... 1133s CAC 1133s CAC 1133s Processing line... 1133s CAC 1133s CAC 1133s Processing line... 1133s CAC 1133s CAC 1133s Processing line... 1133s CAC 1133s CAC 1133s Processing line... 1133s CAC 1133s CAC 1133s Processing line... 1133s CAC 1133s CAC 1133s Processing line... 1133s CAC 1133s CAC 1133s Processing line... 1133s CAC 1133s CAC 1133s Processing line... 1133s /usr/bin/bowtie2 --np 1 --nofw -D 25 -R 4 -N 1 -L22 --rfg 26.4481187300245 --trim5 9 --score-min L,3.91684188085215,5.8604392074688 --cp-min 3 --cp-ival 1 --rdg 9.85136600507708,14.2495042040049 -a --trim3 2 --ma 35.617369123025 --large-index -q -p 4 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1133s --- Summary --- 1133s Read 1 reference strings 1133s Checked 42 alignments, 0 edits 1133s --------------- 1133s PASSED 1133s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1133s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1133s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 1133s Warning: skipping read '2' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1133s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (1) 1133s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1133s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 1133s Warning: skipping mate #1 of read '4' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1133s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (1) 1133s Warning: skipping mate #1 of read '11' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1133s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (1) 1133s Warning: skipping mate #2 of read '23' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1133s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 1133s Warning: skipping read '24' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1133s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 1133s Warning: skipping mate #1 of read '26' because it was < 2 characters long 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1133s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1133s 30 reads; of these: 1133s 25 (83.33%) were paired; of these: 1133s 25 (100.00%) aligned concordantly 0 times 1133s 0 (0.00%) aligned concordantly exactly 1 time 1133s 0 (0.00%) aligned concordantly >1 times 1133s ---- 1133s 25 pairs aligned concordantly 0 times; of these: 1133s 0 (0.00%) aligned discordantly 1 time 1133s ---- 1133s 25 pairs aligned 0 times concordantly or discordantly; of these: 1133s 50 mates make up the pairs; of these: 1133s 42 (84.00%) aligned 0 times 1133s 0 (0.00%) aligned exactly 1 time 1133s 8 (16.00%) aligned >1 times 1133s 5 (16.67%) were unpaired; of these: 1133s 5 (100.00%) aligned 0 times 1133s 0 (0.00%) aligned exactly 1 time 1133s 0 (0.00%) aligned >1 times 1133s 14.55% overall alignment rate 1133s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1133s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1133s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1133s Flattened IUPAC characters 1133s Mutating sequence Sim.pm.2 1133s Introducing 13 SNPs, 2/0 ref/read gaps, and 0 rearrangements 1133s Finished SNPs 1133s Finished ref gaps 1133s Finished read gaps 1133s Mutating sequence Sim.pm.1 1133s Introducing 12 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1133s Finished SNPs 1133s Finished ref gaps 1133s Finished read gaps 1133s Mutated reference genome to subject genome 1133s SNPs introduced: 25 1133s Reference gaps introduced: 2 1133s Read gaps introduced: 0 1133s Rearrangements introduced: 0 1133s Created read sampler 1133s Sampling 90 reads 1133s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1133s *** Run 26 of 100 1133s /usr/bin/bowtie2 --rfg 43.2758429313296,2.07581502452692 --score-min L,2.83104477852527,2.95315332525318 --np 1 --rdg 20.7425731067167 --local --large-index --cp-min 5 --cp-ival 1 --mm -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1133s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1133s parsing sequence Sim.pm.1... 1133s parsing sequence Sim.pm.2... 1133s Parsed 269 reference bases 1133s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1133s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1133s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 1133s Warning: skipping mate #2 of read '9' because it was < 2 characters long 1133s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 1133s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1133s Read 50 alignments... 1133s 90 reads; of these: 1133s 90 (100.00%) were paired; of these: 1133s 90 (100.00%) aligned concordantly 0 times 1133s 0 (0.00%) aligned concordantly exactly 1 time 1133s 0 (0.00%) aligned concordantly >1 times 1133s ---- 1133s 90 pairs aligned concordantly 0 times; of these: 1133s 0 (0.00%) aligned discordantly 1 time 1133s ---- 1133s 90 pairs aligned 0 times concordantly or discordantly; of these: 1133s 180 mates make up the pairs; of these: 1133s 180 (100.00%) aligned 0 times 1133s 0 (0.00%) aligned exactly 1 time 1133s 0 (0.00%) aligned >1 times 1133s 0.00% overall alignment rate 1133s Read 100 alignments... 1133s Read 150 alignments... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s 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Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s /usr/bin/bowtie2 --rfg 43.2758429313296,2.07581502452692 --score-min L,2.83104477852527,2.95315332525318 --np 1 --rdg 20.7425731067167 --local --large-index --cp-min 5 --cp-ival 1 --mm -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s Processing line... 1133s --- Summary --- 1133s Read 1 reference strings 1133s Checked 0 alignments, 0 edits 1133s --------------- 1133s PASSED 1133s ALSO checking that bowtie2 and bowtie2-align match up 1134s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1134s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #2 of read '9' because it was < 2 characters long 1134s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1134s 90 reads; of these: 1134s 90 (100.00%) were paired; of these: 1134s 90 (100.00%) aligned concordantly 0 times 1134s 0 (0.00%) aligned concordantly exactly 1 time 1134s 0 (0.00%) aligned concordantly >1 times 1134s ---- 1134s 90 pairs aligned concordantly 0 times; of these: 1134s 0 (0.00%) aligned discordantly 1 time 1134s ---- 1134s 90 pairs aligned 0 times concordantly or discordantly; of these: 1134s 180 mates make up the pairs; of these: 1134s 180 (100.00%) aligned 0 times 1134s 0 (0.00%) aligned exactly 1 time 1134s 0 (0.00%) aligned >1 times 1134s 0.00% overall alignment rate 1134s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1134s Flattened IUPAC characters 1134s Mutating sequence Sim.pm.2 1134s Introducing 14 SNPs, 0/3 ref/read gaps, and 1 rearrangements 1134s Finished SNPs 1134s Finished ref gaps 1134s Finished read gaps 1134s Mutating sequence Sim.pm.1 1134s Introducing 6 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1134s Finished SNPs 1134s Finished ref gaps 1134s Finished read gaps 1134s Mutated reference genome to subject genome 1134s SNPs introduced: 20 1134s Reference gaps introduced: 0 1134s Read gaps introduced: 5 1134s Rearrangements introduced: 1 1134s Created read sampler 1134s Sampling 106 reads 1134s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1134s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1134s parsing sequence Sim.pm.1... 1134s parsing sequence Sim.pm.2... 1134s Parsed 269 reference bases 1134s *** Run 27 of 100 1134s /usr/bin/bowtie2 -D 20 --np 1 --nofw --score-min L,7.53842543660019,9.47244446452604 --cp-ival 1 --mm --cp-min 5 --large-index -M 2 --mp 8.7583362303947,2.12685746596329 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1134s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1134s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1134s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1134s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #2 of read '30' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1134s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #2 of read '33' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1134s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1134s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #2 of read '57' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1134s Read 50 alignments... 1134s Read 100 alignments... 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1134s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #2 of read '87' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1134s Read 150 alignments... 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1134s 106 reads; of these: 1134s 106 (100.00%) were paired; of these: 1134s 104 (98.11%) aligned concordantly 0 times 1134s 0 (0.00%) aligned concordantly exactly 1 time 1134s 2 (1.89%) aligned concordantly >1 times 1134s ---- 1134s 104 pairs aligned concordantly 0 times; of these: 1134s 0 (0.00%) aligned discordantly 1 time 1134s ---- 1134s 104 pairs aligned 0 times concordantly or discordantly; of these: 1134s 208 mates make up the pairs; of these: 1134s 194 (93.27%) aligned 0 times 1134s 1 (0.48%) aligned exactly 1 time 1134s 13 (6.25%) aligned >1 times 1134s 8.49% overall alignment rate 1134s Read 200 alignments... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s CGT 1134s CGT 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s TCACAT 1134s TCACAT 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s TGTCACATCGA 1134s TGTCACATCGA 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s CGAG 1134s CGAG 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s ATCGAGATGGAC 1134s ATCGAGATGGAC 1134s Processing line... 1134s Processing line... 1134s ACGC 1134s ACGC 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s AG 1134s AG 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s GATA 1134s GATA 1134s Processing line... 1134s Processing line... 1134s CACGA 1134s CACGA 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s ACCTC 1134s ACCTC 1134s Processing line... 1134s Processing line... 1134s CGAGCCTGTCAC 1134s CGAGCCTGTCAC 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s ACC 1134s ACC 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s CATCG 1134s CATCG 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s ACATCGAG 1134s ACATCGAG 1134s Processing line... 1134s CCACCTCGTGGG 1134s CCACCTCGTGGG 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s GAACACGAGCCTGTC 1134s GAACACGAGCCTGTC 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s CA 1134s CA 1134s Processing line... 1134s CG 1134s CG 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s Processing line... 1134s --- Summary --- 1134s Read 1 reference strings 1134s Checked 18 alignments, 0 edits 1134s --------------- 1134s PASSED 1134s ALSO checking that bowtie2 and bowtie2-align match up 1134s /usr/bin/bowtie2 -D 20 --np 1 --nofw --score-min L,7.53842543660019,9.47244446452604 --cp-ival 1 --mm --cp-min 5 --large-index -M 2 --mp 8.7583362303947,2.12685746596329 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1134s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1134s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1134s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1134s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #2 of read '30' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1134s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #2 of read '33' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1134s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1134s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #2 of read '57' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1134s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 1134s Warning: skipping mate #2 of read '87' because it was < 2 characters long 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1134s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1134s 106 reads; of these: 1134s 106 (100.00%) were paired; of these: 1134s 104 (98.11%) aligned concordantly 0 times 1134s 0 (0.00%) aligned concordantly exactly 1 time 1134s 2 (1.89%) aligned concordantly >1 times 1134s ---- 1134s 104 pairs aligned concordantly 0 times; of these: 1134s 0 (0.00%) aligned discordantly 1 time 1134s ---- 1134s 104 pairs aligned 0 times concordantly or discordantly; of these: 1134s 208 mates make up the pairs; of these: 1134s 194 (93.27%) aligned 0 times 1134s 1 (0.48%) aligned exactly 1 time 1134s 13 (6.25%) aligned >1 times 1134s 8.49% overall alignment rate 1134s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1134s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1134s /usr/bin/bowtie2 -D 20 --np 1 --nofw --score-min L,7.53842543660019,9.47244446452604 --cp-ival 1 --mm --cp-min 5 --large-index -M 2 --mp 8.7583362303947,2.12685746596329 -r -p 3 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1135s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1135s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 1135s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1135s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 1135s Warning: skipping mate #2 of read '33' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1135s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 1135s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1135s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 1135s Warning: skipping mate #1 of read '56' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1135s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 1135s Warning: skipping mate #2 of read '57' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1135s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 1135s Warning: skipping mate #2 of read '30' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1135s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 1135s Warning: skipping mate #2 of read '87' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1135s 106 reads; of these: 1135s 106 (100.00%) were paired; of these: 1135s 104 (98.11%) aligned concordantly 0 times 1135s 0 (0.00%) aligned concordantly exactly 1 time 1135s 2 (1.89%) aligned concordantly >1 times 1135s ---- 1135s 104 pairs aligned concordantly 0 times; of these: 1135s 0 (0.00%) aligned discordantly 1 time 1135s ---- 1135s 104 pairs aligned 0 times concordantly or discordantly; of these: 1135s 208 mates make up the pairs; of these: 1135s 194 (93.27%) aligned 0 times 1135s 1 (0.48%) aligned exactly 1 time 1135s 13 (6.25%) aligned >1 times 1135s 8.49% overall alignment rate 1135s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1135s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1135s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1135s Flattened IUPAC characters 1135s Mutating sequence Sim.pm.2 1135s Introducing 16 SNPs, 3/2 ref/read gaps, and 1 rearrangements 1135s Finished SNPs 1135s Finished ref gaps 1135s Finished read gaps 1135s Mutating sequence Sim.pm.1 1135s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1135s Finished SNPs 1135s Finished ref gaps 1135s Finished read gaps 1135s Mutated reference genome to subject genome 1135s SNPs introduced: 19 1135s Reference gaps introduced: 3 1135s Read gaps introduced: 2 1135s Rearrangements introduced: 1 1135s Created read sampler 1135s Sampling 121 reads 1135s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1135s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1135s parsing sequence Sim.pm.1... 1135s parsing sequence Sim.pm.2... 1135s Parsed 269 reference bases 1135s *** Run 28 of 100 1135s /usr/bin/bowtie2 --score-min L,1.06861737595521,3.07683633711705 --trim5 5 -i S,0.303941739180613 -R 1 --np 2 --ma 32.4555444045557 --large-index -M 2 --rdg 15.7784538809995 --trim3 0 --mm --cp-ival 2 --cp-min 2 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1135s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1135s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1135s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '10' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1135s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 1135s Warning: skipping read '18' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1135s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '23' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1135s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 1135s Warning: skipping read '31' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1135s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '32' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1135s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '33' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1135s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '39' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1135s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '40' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1135s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '47' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1135s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '48' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1135s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '53' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1135s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '54' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1135s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '69' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1135s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 1135s Warning: skipping read '71' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1135s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '77' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1135s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '84' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1135s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '86' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1135s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 1135s Warning: skipping read '89' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1135s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '95' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1135s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '97' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1135s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '109' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1135s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '117' because it was < 2 characters long 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1135s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1135s 121 reads; of these: 1135s 121 (100.00%) were unpaired; of these: 1135s 97 (80.17%) aligned 0 times 1135s 8 (6.61%) aligned exactly 1 time 1135s 16 (13.22%) aligned >1 times 1135s 19.83% overall alignment rate 1135s Read 50 alignments... 1135s Read 100 alignments... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s GGGTATGG 1135s GGGTATGG 1135s Processing line... 1135s Processing line... 1135s CATCGAGAT 1135s CATCGAGAT 1135s Processing line... 1135s Processing line... 1135s AG 1135s AG 1135s Processing line... 1135s CATCGAGAT 1135s CATCGAGAT 1135s Processing line... 1135s GCGTAA 1135s GCGTAA 1135s Processing line... 1135s AAATTA 1135s AAATTA 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s ACC 1135s ACC 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s GCGGCTG 1135s GCGGCTG 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s TTAGAGCT 1135s TTAGAGCT 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s CAC 1135s CAC 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s GACCACCTCG 1135s GACCACCTCG 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s ACACGAGCCTGTCAC 1135s ACACGAGCCTGTCAC 1135s Processing line... 1135s Processing line... 1135s GAAG 1135s GAAG 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s ATTAG 1135s ATTAG 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s GA 1135s GA 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s TCACATCGAGA 1135s TCACATCGAGA 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s TTAGAGCT 1135s TTAGAGCT 1135s Processing line... 1135s Processing line... 1135s AGC 1135s AGC 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s AAC 1135s AAC 1135s Processing line... 1135s ACCACCTCG 1135s ACCACCTCG 1135s Processing line... 1135s AAA 1135s AAA 1135s Processing line... 1135s GAGATGGACCACC 1135s GAGATGGACCACC 1135s Processing line... 1135s Processing line... 1135s CCTCGTGGG 1135s CCTCGTGGG 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s AAA 1135s AAA 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s --- Summary --- 1135s Read 1 reference strings 1135s Checked 24 alignments, 0 edits 1135s --------------- 1135s PASSED 1135s Flattened IUPAC characters 1135s Mutating sequence Sim.pm.1 1135s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1135s Finished SNPs 1135s Finished ref gaps 1135s Finished read gaps 1135s Mutating sequence Sim.pm.2 1135s Introducing 20 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1135s Finished SNPs 1135s Finished ref gaps 1135s Finished read gaps 1135s Mutated reference genome to subject genome 1135s SNPs introduced: 21 1135s Reference gaps introduced: 1 1135s Read gaps introduced: 0 1135s Rearrangements introduced: 0 1135s Created read sampler 1135s Sampling 66 reads 1135s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1135s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1135s parsing sequence Sim.pm.1... 1135s parsing sequence Sim.pm.2... 1135s Parsed 269 reference bases 1135s *** Run 29 of 100 1135s /usr/bin/bowtie2 -R 4 --np 2 --score-min L,7.07290414264279,5.33098077454295 --rfg 32.2867361835076,17.1756017245008 --trim5 6 --cp-ival 3 --cp-min 2 --large-index --local --rdg 23.8230223562368,12.4540226220116 --mp 2.3587098645467,1.66316823818223 --trim3 6 -a -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1135s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '1' because it was < 2 characters long 1135s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '3' because it was < 2 characters long 1135s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '6' because it was < 2 characters long 1135s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '9' because it was < 2 characters long 1135s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '13' because it was < 2 characters long 1135s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '18' because it was < 2 characters long 1135s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '19' because it was < 2 characters long 1135s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 1135s Warning: skipping read '20' because it was < 2 characters long 1135s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '22' because it was < 2 characters long 1135s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '23' because it was < 2 characters long 1135s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '25' because it was < 2 characters long 1135s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '30' because it was < 2 characters long 1135s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '31' because it was < 2 characters long 1135s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '39' because it was < 2 characters long 1135s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '40' because it was < 2 characters long 1135s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '41' because it was < 2 characters long 1135s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '46' because it was < 2 characters long 1135s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '47' because it was < 2 characters long 1135s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '50' because it was < 2 characters long 1135s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 1135s Warning: skipping read '51' because it was < 2 characters long 1135s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '57' because it was < 2 characters long 1135s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '59' because it was < 2 characters long 1135s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '60' because it was < 2 characters long 1135s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '61' because it was < 2 characters long 1135s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '65' because it was < 2 characters long 1135s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '66' because it was < 2 characters long 1135s 66 reads; of these: 1135s 66 (100.00%) were unpaired; of these: 1135s 66 (100.00%) aligned 0 times 1135s 0 (0.00%) aligned exactly 1 time 1135s 0 (0.00%) aligned >1 times 1135s 0.00% overall alignment rate 1135s Read 50 alignments... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s Processing line... 1135s --- Summary --- 1135s Read 1 reference strings 1135s Checked 0 alignments, 0 edits 1135s --------------- 1135s PASSED 1135s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1135s /usr/bin/bowtie2 -R 4 --np 2 --score-min L,7.07290414264279,5.33098077454295 --rfg 32.2867361835076,17.1756017245008 --trim5 6 --cp-ival 3 --cp-min 2 --large-index --local --rdg 23.8230223562368,12.4540226220116 --mp 2.3587098645467,1.66316823818223 --trim3 6 -a -q -p 4 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1135s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '1' because it was < 2 characters long 1135s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '3' because it was < 2 characters long 1135s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '6' because it was < 2 characters long 1135s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '9' because it was < 2 characters long 1135s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '13' because it was < 2 characters long 1135s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '18' because it was < 2 characters long 1135s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '19' because it was < 2 characters long 1135s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 1135s Warning: skipping read '20' because it was < 2 characters long 1135s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '22' because it was < 2 characters long 1135s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '23' because it was < 2 characters long 1135s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '25' because it was < 2 characters long 1135s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '30' because it was < 2 characters long 1135s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '31' because it was < 2 characters long 1135s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '39' because it was < 2 characters long 1135s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '40' because it was < 2 characters long 1135s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '41' because it was < 2 characters long 1135s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '46' because it was < 2 characters long 1135s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '47' because it was < 2 characters long 1135s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '50' because it was < 2 characters long 1135s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 1135s Warning: skipping read '51' because it was < 2 characters long 1135s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '57' because it was < 2 characters long 1135s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '59' because it was < 2 characters long 1135s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '60' because it was < 2 characters long 1135s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '61' because it was < 2 characters long 1135s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '65' because it was < 2 characters long 1135s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1135s Warning: skipping read '66' because it was < 2 characters long 1135s 66 reads; of these: 1135s 66 (100.00%) were unpaired; of these: 1135s 66 (100.00%) aligned 0 times 1135s 0 (0.00%) aligned exactly 1 time 1135s 0 (0.00%) aligned >1 times 1135s 0.00% overall alignment rate 1135s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1136s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1136s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1136s Flattened IUPAC characters 1136s Mutating sequence Sim.pm.1 1136s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1136s Finished SNPs 1136s Finished ref gaps 1136s Finished read gaps 1136s Mutating sequence Sim.pm.2 1136s Introducing 26 SNPs, 0/1 ref/read gaps, and 2 rearrangements 1136s Finished SNPs 1136s Finished ref gaps 1136s Finished read gaps 1136s Mutated reference genome to subject genome 1136s SNPs introduced: 28 1136s Reference gaps introduced: 1 1136s Read gaps introduced: 1 1136s Rearrangements introduced: 2 1136s Created read sampler 1136s Sampling 87 reads 1136s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1136s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1136s parsing sequence Sim.pm.1... 1136s parsing sequence Sim.pm.2... 1136s Parsed 269 reference bases 1136s *** Run 30 of 100 1136s /usr/bin/bowtie2 -a --trim3 0 --score-min L,9.68315473108932,8.4776787821216 --large-index --nofw --cp-min 4 --cp-ival 1 --mm -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1136s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 1136s Warning: skipping read '82' because it was < 2 characters long 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1136s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1136s 87 reads; of these: 1136s 87 (100.00%) were unpaired; of these: 1136s 77 (88.51%) aligned 0 times 1136s 5 (5.75%) aligned exactly 1 time 1136s 5 (5.75%) aligned >1 times 1136s 11.49% overall alignment rate 1136s Read 50 alignments... 1136s Read 100 alignments... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s AATT 1136s AATT 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s GC 1136s GC 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s TGT 1136s TGT 1136s Processing line... 1136s TGT 1136s TGT 1136s Processing line... 1136s TGT 1136s TGT 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s TGT 1136s TGT 1136s Processing line... 1136s TGT 1136s TGT 1136s Processing line... 1136s TGT 1136s TGT 1136s Processing line... 1136s Processing line... 1136s GTATGGTGAGGG 1136s GTATGGTGAGGG 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s CATCGAGATGGACCACCTCG 1136s CATCGAGATGGACCACCTCG 1136s Processing line... 1136s CATCGAGATGGACCACCTCG 1136s CATCGAGATGGACCACCTCG 1136s Processing line... 1136s CATCGAGATGGACCACCTCG 1136s CATCGAGATGGACCACCTCG 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s CGAC 1136s CGAC 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s GTG 1136s GTG 1136s Processing line... 1136s GTG 1136s GTG 1136s Processing line... 1136s GTG 1136s GTG 1136s Processing line... 1136s GTG 1136s GTG 1136s Processing line... 1136s GTG 1136s GTG 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s AATTAGAGC 1136s AATTAGAGC 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s GCTGAA 1136s GCTGAA 1136s Processing line... 1136s Processing line... 1136s --- Summary --- 1136s Read 1 reference strings 1136s Checked 30 alignments, 0 edits 1136s --------------- 1136s PASSED 1136s Flattened IUPAC characters 1136s Mutating sequence Sim.pm.1 1136s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1136s Finished SNPs 1136s Finished ref gaps 1136s Finished read gaps 1136s Mutating sequence Sim.pm.2 1136s Introducing 6 SNPs, 1/1 ref/read gaps, and 1 rearrangements 1136s Finished SNPs 1136s Finished ref gaps 1136s Finished read gaps 1136s Mutated reference genome to subject genome 1136s SNPs introduced: 9 1136s *** Run 31 of 100 1136s /usr/bin/bowtie2 --rfg 20.8429571802967,9.23127272988585 -i S,2.36216551474485,1.15148200321755 --score-min L,2.62947693909776,5.36942263571589 --norc -D 43 --trim3 2 --rdg 40.2099851606641 --local --large-index -M 6 --cp-min 5 --cp-ival 2 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq 1136s Reference gaps introduced: 1 1136s Read gaps introduced: 1 1136s Rearrangements introduced: 1 1136s Created read sampler 1136s Sampling 82 reads 1136s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1136s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1136s parsing sequence Sim.pm.1... 1136s parsing sequence Sim.pm.2... 1136s Parsed 269 reference bases 1136s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1136s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1136s Warning: skipping mate #2 of read 'R_1_1_1_35_35_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #2 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1136s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1136s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1136s Read 50 alignments... 1136s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1136s Warning: skipping mate #2 of read 'R_1_1_1_79_79_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #2 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1136s 82 reads; of these: 1136s 78 (95.12%) were paired; of these: 1136s 78 (100.00%) aligned concordantly 0 times 1136s 0 (0.00%) aligned concordantly exactly 1 time 1136s 0 (0.00%) aligned concordantly >1 times 1136s ---- 1136s 78 pairs aligned concordantly 0 times; of these: 1136s 0 (0.00%) aligned discordantly 1 time 1136s ---- 1136s 78 pairs aligned 0 times concordantly or discordantly; of these: 1136s 156 mates make up the pairs; of these: 1136s 156 (100.00%) aligned 0 times 1136s 0 (0.00%) aligned exactly 1 time 1136s 0 (0.00%) aligned >1 times 1136s 4 (4.88%) were unpaired; of these: 1136s 4 (100.00%) aligned 0 times 1136s 0 (0.00%) aligned exactly 1 time 1136s 0 (0.00%) aligned >1 times 1136s 0.00% overall alignment rate 1136s Read 100 alignments... 1136s Read 150 alignments... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s /usr/bin/bowtie2 --rfg 20.8429571802967,9.23127272988585 -i S,2.36216551474485,1.15148200321755 --score-min L,2.62947693909776,5.36942263571589 --norc -D 43 --trim3 2 --rdg 40.2099851606641 --local --large-index -M 6 --cp-min 5 --cp-ival 2 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s Processing line... 1136s --- Summary --- 1136s Read 1 reference strings 1136s Checked 0 alignments, 0 edits 1136s --------------- 1136s PASSED 1136s ALSO checking that bowtie2 and bowtie2-align match up 1136s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1136s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1136s Warning: skipping mate #2 of read 'R_1_1_1_35_35_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #2 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1136s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1136s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1136s Warning: skipping mate #2 of read 'R_1_1_1_79_79_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #2 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1136s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 1136s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1136s 82 reads; of these: 1136s 78 (95.12%) were paired; of these: 1136s 78 (100.00%) aligned concordantly 0 times 1136s 0 (0.00%) aligned concordantly exactly 1 time 1136s 0 (0.00%) aligned concordantly >1 times 1136s ---- 1136s 78 pairs aligned concordantly 0 times; of these: 1136s 0 (0.00%) aligned discordantly 1 time 1136s ---- 1136s 78 pairs aligned 0 times concordantly or discordantly; of these: 1136s 156 mates make up the pairs; of these: 1136s 156 (100.00%) aligned 0 times 1136s 0 (0.00%) aligned exactly 1 time 1136s 0 (0.00%) aligned >1 times 1136s 4 (4.88%) were unpaired; of these: 1136s 4 (100.00%) aligned 0 times 1136s 0 (0.00%) aligned exactly 1 time 1136s 0 (0.00%) aligned >1 times 1136s 0.00% overall alignment rate 1136s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1136s Flattened IUPAC characters 1136s Mutating sequence Sim.pm.2 1136s Introducing 22 SNPs, 1/2 ref/read gaps, and 4 rearrangements 1136s Finished SNPs 1136s Finished ref gaps 1136s Finished read gaps 1136s Mutating sequence Sim.pm.1 1136s Introducing 7 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1136s Finished SNPs 1136s Finished ref gaps 1136s Finished read gaps 1136s Mutated reference genome to subject genome 1136s SNPs introduced: 29 1136s Reference gaps introduced: 1 1136s Read gaps introduced: 2 1136s Rearrangements introduced: 6 1136s Created read sampler 1136s Sampling 121 reads 1136s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1136s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1136s parsing sequence Sim.pm.1... 1136s parsing sequence Sim.pm.2... 1136s Parsed 269 reference bases 1136s *** Run 32 of 100 1136s /usr/bin/bowtie2 --large-index --ma 19.4972746210491 -a --mp 9.53146710906863,4.42565336366209 --trim3 5 --cp-ival 1 --cp-min 4 --score-min L,7.26474081003246,6.31840193554022 --n-ceil 0.057025400384869,0.685496204889928 --rfg 27.4470316823561,12.1362982264652 --trim5 5 -D 44 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1137s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1137s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '1' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1137s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '6' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1137s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '8' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1137s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '14' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1137s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '19' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1137s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '23' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1137s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '27' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1137s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '35' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1137s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '36' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1137s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '37' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1137s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '42' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1137s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 1137s Warning: skipping read '43' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1137s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '45' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1137s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '47' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1137s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '49' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1137s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '51' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1137s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '56' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1137s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '60' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1137s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '64' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1137s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '65' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1137s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '66' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1137s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '68' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1137s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '72' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1137s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '75' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1137s Read 50 alignments... 1137s Read 100 alignments... 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1137s Warning: skipping read '83' because length (1) <= # seed mismatches (0) 1137s Warning: skipping read '83' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1137s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '89' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1137s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '90' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1137s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '93' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1137s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '96' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1137s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '97' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1137s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '104' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1137s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '105' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1137s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '106' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1137s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '107' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1137s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '108' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1137s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '111' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1137s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '113' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1137s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '115' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1137s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '120' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1137s 121 reads; of these: 1137s 121 (100.00%) were unpaired; of these: 1137s 111 (91.74%) aligned 0 times 1137s 3 (2.48%) aligned exactly 1 time 1137s 7 (5.79%) aligned >1 times 1137s 8.26% overall alignment rate 1137s Read 150 alignments... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s TG 1137s TG 1137s Processing line... 1137s CA 1137s CA 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s CAGCGC 1137s CAGCGC 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s AGG 1137s AGG 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s CCT 1137s CCT 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s TCGAG 1137s TCGAG 1137s Processing line... 1137s TCGAG 1137s TCGAG 1137s Processing line... 1137s TCGAG 1137s TCGAG 1137s Processing line... 1137s TCGAG 1137s TCGAG 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s /usr/bin/bowtie2 --large-index --ma 19.4972746210491 -a --mp 9.53146710906863,4.42565336366209 --trim3 5 --cp-ival 1 --cp-min 4 --score-min L,7.26474081003246,6.31840193554022 --n-ceil 0.057025400384869,0.685496204889928 --rfg 27.4470316823561,12.1362982264652 --trim5 5 -D 44 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s GAACACGAGCCT 1137s GAACACGAGCCT 1137s Processing line... 1137s GAACACGAGCCT 1137s GAACACGAGCCT 1137s Processing line... 1137s GAACACGAGCCT 1137s GAACACGAGCCT 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s AAGTGGCTG 1137s AAGTGGCTG 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s ATAACCAA 1137s ATAACCAA 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s --- Summary --- 1137s Read 1 reference strings 1137s Checked 81 alignments, 0 edits 1137s --------------- 1137s PASSED 1137s ALSO checking that bowtie2 and bowtie2-align match up 1137s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1137s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '1' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1137s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '6' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1137s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '8' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1137s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '14' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1137s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '19' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1137s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '23' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1137s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '27' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1137s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '35' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1137s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '36' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1137s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '37' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1137s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '42' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1137s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 1137s Warning: skipping read '43' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1137s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '45' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1137s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '47' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1137s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '49' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1137s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '51' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1137s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '56' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1137s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '60' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1137s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '64' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1137s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '65' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1137s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '66' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1137s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '68' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1137s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '72' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1137s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '75' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1137s Warning: skipping read '83' because length (1) <= # seed mismatches (0) 1137s Warning: skipping read '83' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1137s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '89' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1137s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '90' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1137s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '93' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1137s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '96' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1137s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '97' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1137s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '104' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1137s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '105' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1137s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '106' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1137s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '107' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1137s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '108' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1137s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '111' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1137s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '113' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1137s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '115' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1137s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 1137s Warning: skipping read '120' because it was < 2 characters long 1137s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1137s 121 reads; of these: 1137s 121 (100.00%) were unpaired; of these: 1137s 111 (91.74%) aligned 0 times 1137s 3 (2.48%) aligned exactly 1 time 1137s 7 (5.79%) aligned >1 times 1137s 8.26% overall alignment rate 1137s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1137s Flattened IUPAC characters 1137s Mutating sequence Sim.pm.1 1137s Introducing 4 SNPs, 0/2 ref/read gaps, and 1 rearrangements 1137s Finished SNPs 1137s Finished ref gaps 1137s Finished read gaps 1137s Mutating sequence Sim.pm.2 1137s Introducing 22 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1137s Finished SNPs 1137s Finished ref gaps 1137s Finished read gaps 1137s Mutated reference genome to subject genome 1137s SNPs introduced: 26 1137s Reference gaps introduced: 1 1137s Read gaps introduced: 2 1137s Rearrangements introduced: 2 1137s Created read sampler 1137s Sampling 70 reads 1137s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1137s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1137s parsing sequence Sim.pm.1... 1137s *** Run 33 of 100 1137s /usr/bin/bowtie2 --score-min L,3.67289173425911,1.06197940710385 --n-ceil 0.70975622480236,1.34476699135508 --large-index --local -a --cp-ival 1 -D 38 --np 1 --cp-min 4 --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1137s parsing sequence Sim.pm.2... 1137s Parsed 269 reference bases 1137s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 1137s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1137s Read 50 alignments... 1137s 70 reads; of these: 1137s 70 (100.00%) were unpaired; of these: 1137s 37 (52.86%) aligned 0 times 1137s 8 (11.43%) aligned exactly 1 time 1137s 25 (35.71%) aligned >1 times 1137s 47.14% overall alignment rate 1137s Read 100 alignments... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s CCTGTCACCTCGAGAT 1137s CCTGTCACATCGAGAT 1137s Processing line... 1137s CCTGTCACCTCGAGAT 1137s CCTGTCACATCGAGAT 1137s Processing line... 1137s CCTGTCACCTCGAGAT 1137s CCTGTCACATCGAGAT 1137s Processing line... 1137s Processing line... 1137s AACCAGAGTAGAACACGAGCCTGTCACCTCGAGATGGACCACCTCGTGGGGTGG 1137s AACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGT-GGGNTG 1137s Processing line... 1137s AACCAGAGTAGAACACGAGCCTGTCACCTCGAGATGGACCACCTCGTGGGGTGG 1137s AACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGT-GGGNTG 1137s Processing line... 1137s AACCAGAGTAGAACACGAGCCTGTCACCTCGAGATGGACCACCTCGTGGGGTGG 1137s AACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGT-GGGNTG 1137s Processing line... 1137s AGCCTGTCACATCGAGATGGACCACCACGTGGGGTGGATACCCAAAAC---G 1137s AGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAACGCNG 1137s Processing line... 1137s AGCCTGTCACATCGAGATGGACCACCACGTGGGGTGGAT-AC 1137s AGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAAC 1137s Processing line... 1137s AGCCTGTCACATCGAGATGGACCACCACGTGGGGTGGAT-AC 1137s AGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAAC 1137s Processing line... 1137s AGAAAACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGATAACCAAAACGCCGAAATTAGAGCTCGCAGCGCGTAAAA------G 1137s AGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAACGCNGAAATTAGAGCTCGCAGCGCGTAANAGGGNGGG 1137s Processing line... 1137s AGCCTGTCACATC 1137s AGCCTGTCACATC 1137s Processing line... 1137s AGCCTGTCACATC 1137s AGCCTGTCACATC 1137s Processing line... 1137s AGCCTGTCACATC 1137s AGCCTGTCACATC 1137s Processing line... 1137s Processing line... 1137s CCATAGTAGAACACGAGCCTGTCACAGCGAGATGGACTACCTCGTGGGCTGAATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCACGTGGGGTGGATACCC-------A 1137s CCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGA 1137s Processing line... 1137s CCATAGTAGAACACGAGCCTGTCACAGCGAGATGGACTACCTCGTGGGCTGAATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCACGTGGGGTGGATACCCA 1137s CCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGG------A 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s GAGGGGTATGGTGAGGGTCGAGGAC 1137s GNGGGGTATGGTGAGGGTCGAGGAC 1137s Processing line... 1137s CGAGATGGACCACCACGTGGG 1137s CGAGATGGACCACCTCGTGGG 1137s Processing line... 1137s CGAGATGGACCACCACGTGGG 1137s CGAGATGGACCACCTCGTGGG 1137s Processing line... 1137s CGAGATGGACCACCACGTGGG 1137s CGAGATGGACCACCTCGTGGG 1137s Processing line... 1137s CTCGTGGGCTGGATAACCATAGTAGAACACGAGCCTGTCACAGCGAGATGGACTACCTCGTGGGCTGAATAACCACAGTAGAACACGAGCCTGTCACATC 1137s CTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCA---C 1137s Processing line... 1137s GGATAACCATAGTAGAACACGAGCCTGTCACAGCGAGATGGACTACCTCGTGGGCTGAATAACCACAGTAGAACACGAGCCTGTCACATC 1137s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCA---C 1137s Processing line... 1137s CTCGTGGGCTGGATAACCATAGTAGAACACGAGCCTGTCACAGCGAGATGGACTACCTCGTGGGCTGAATAACCA 1137s CTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCA 1137s Processing line... 1137s GGATAACCAGAGTAGAACACGAGCCTGTCACCTCGAGATGGACCACCTCGTGGGGTGGATAACCATAGTCGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATAACCATA 1137s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACC--A 1137s Processing line... 1137s GGATAACCAGAGTAGAACACGAGCCTGTCACCTCGAGATGGACCACCTCGTGGGGTGGATAACCATAGTCGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATAACCATAGTA 1137s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAA--A 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s CGC 1137s CGC 1137s Processing line... 1137s GCG 1137s GCG 1137s Processing line... 1137s GCG 1137s GCG 1137s Processing line... 1137s GCG 1137s GCG 1137s Processing line... 1137s CGC 1137s CGC 1137s Processing line... 1137s CGC 1137s CGC 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s TGGGCTGGATAACCATAGTAGAACACGAGCCTGTCACAGCGAGATGGACTACCTCGTGGGCTGAATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCACGTGGGGTGGATACCCAAAACGCCGAAGTTAGAGCTCGCAGCGCG-A 1137s TGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAACGCNGAAATTAGAGCTCGCAGCGCGTA 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s GATAACCATAGTCGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATAACCATAGTAGAAAACGAGCCTGTCACATCGAGATG 1137s GATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGA---G 1137s Processing line... 1137s GATAACCATAGTCGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATAACCATAGTAGAAAACGAGCCTGTCACATCGAGATG 1137s GATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGA---G 1137s Processing line... 1137s GATAACCATAGTCGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATAACCA 1137s GATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCA 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s GGATAACCAGAGTAGAACACGAGCCTGTCACCTCGAGATGGACCACCTCGTGGGGTGGATAACCATAGTCGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATAACCATAGTAGAAA 1137s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAG-AA 1137s Processing line... 1137s TGGATA 1137s TGGATA 1137s Processing line... 1137s TGGATA 1137s TGGATA 1137s Processing line... 1137s TGGATA 1137s TGGATA 1137s Processing line... 1137s AAAACGCCGAAGTTAGAGCTCGCAGCGCGAAAGAGGGAGGGGTATGGTGAGGGTCGAGGAC 1137s AAAACGCNGAAATTAGAGCTCGCAGCGCGTAANAGGGNGGGGTATGGTGAGGGTCGAGGAC 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s CCAAA 1137s CCAAA 1137s Processing line... 1137s Processing line... 1137s ACGAGCCTGTCACATCGAGATGGACCACCTCGTGGG 1137s ACGAGCCTGTCACATCGAGATGGACCACCTCGT-GG 1137s Processing line... 1137s ACGAGCCTGTCACATCGAGATGGACCACCTCGTGGG 1137s ACGAGCCTGTCACATCGAGATGGACCACCTCGT-GG 1137s Processing line... 1137s ACGAGCCTGTCACATCGAGATGGACCACCTCGTGGG 1137s ACGAGCCTGTCACATCGAGATGGACCACCTCGT-GG 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s CACGAGCCTG 1137s CACGAGCCTG 1137s Processing line... 1137s CACGAGCCTG 1137s CACGAGCCTG 1137s Processing line... 1137s CACGAGCCTG 1137s CACGAGCCTG 1137s Processing line... 1137s Processing line... 1137s AGATGGA 1137s AGATGGA 1137s Processing line... 1137s AGATGGA 1137s AGATGGA 1137s Processing line... 1137s AGATGGA 1137s AGATGGA 1137s Processing line... 1137s GTCACATCGAGATGGACCACC 1137s GTCACATCGAGATGGACCA-C 1137s Processing line... 1137s /usr/bin/bowtie2 --score-min L,3.67289173425911,1.06197940710385 --n-ceil 0.70975622480236,1.34476699135508 --large-index --local -a --cp-ival 1 -D 38 --np 1 --cp-min 4 --qseq -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1137s GTCACATCGAGATGGACCACC 1137s GTCACATCGAGATGGACCA-C 1137s Processing line... 1137s GTCACATCGAGATGGACCACC 1137s GTCACATCGAGATGGACCA-C 1137s Processing line... 1137s CTGTCACATCGAGATGGACCACCTCGTGGGTTGGATTACCATAGTAGACCACGAGCCTGTCACATCCGGA-TG 1137s CTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGG 1137s Processing line... 1137s CTGTCACATCGAGATGGACCACCTCGTGGGTTGGATTACCATAGTAGACCACGAGCCTGTCACATCCGGA-TG 1137s CTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGG 1137s Processing line... 1137s GAGCCTGTCACA 1137s GAGCCTGTCACA 1137s Processing line... 1137s GAGCCTGTCACA 1137s GAGCCTGTCACA 1137s Processing line... 1137s GAGCCTGTCACA 1137s GAGCCTGTCACA 1137s Processing line... 1137s GAGATG 1137s GAGATG 1137s Processing line... 1137s GAGATG 1137s GAGATG 1137s Processing line... 1137s GAGATG 1137s GAGATG 1137s Processing line... 1137s GTGGGCTGGATAACCATAGTAGAACACGAGCCTGTCACAGCGAGATGGACTAC 1137s GTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGG---AC 1137s Processing line... 1137s GTGGGCTGGATAACCATAGTAGAACACGAGCCTGTCACAGCGAGATGGACTAC 1137s GTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGG---AC 1137s Processing line... 1137s GGATAACCATAGTAGAACACGAGCCTGTCACAGCGAGATGGA-C 1137s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACC 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s TCA 1137s TCA 1137s Processing line... 1137s TGA 1137s TGA 1137s Processing line... 1137s TGA 1137s TGA 1137s Processing line... 1137s TCA 1137s TCA 1137s Processing line... 1137s TCA 1137s TCA 1137s Processing line... 1137s TGA 1137s TGA 1137s Processing line... 1137s Processing line... 1137s ATTAGAGCTCGCAGCGCGTAAAAGGGTGGGGTATGGTGAGG 1137s ATTAGAGCTCGCAGCGCGTAANAGGGNGGGGTATGGTGA-G 1137s Processing line... 1137s Processing line... 1137s CGAGCCTGTCACAGCGAGATGGACTACCTCGTGGGCTGAATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCACGTGGGGTGG------A 1137s CGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCA 1137s Processing line... 1137s CGAGCCTGTCACAGCGAGATGGACTACCTCGTGGGCTGAATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCACGTGGGGTGG------A 1137s CGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCA 1137s Processing line... 1137s TCACATCGAGATGGACCACCACGTGGG 1137s TCACATCGAGATGGACCACCTCGT-GG 1137s Processing line... 1137s TCACATCGAGATGGACCACCACGTGGG 1137s TCACATCGAGATGGACCACCTCGT-GG 1137s Processing line... 1137s TCACATCGAGATGGACCACCACGTGGG 1137s TCACATCGAGATGGACCACCTCGT-GG 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s TGTCACATCGA 1137s TGTCACATCGA 1137s Processing line... 1137s TGTCACATCGA 1137s TGTCACATCGA 1137s Processing line... 1137s TGTCACATCGA 1137s TGTCACATCGA 1137s Processing line... 1137s Processing line... 1137s CCTGTCACCTCGAGAT 1137s CCTGTCACATCGAGAT 1137s Processing line... 1137s CCTGTCACCTCGAGAT 1137s CCTGTCACATCGAGAT 1137s Processing line... 1137s CCTGTCACCTCGAGAT 1137s CCTGTCACATCGAGAT 1137s Processing line... 1137s Processing line... 1137s Processing line... 1137s CACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGG--A 1137s CACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATA 1137s Processing line... 1137s CACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGG--A 1137s CACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATA 1137s Processing line... 1137s CACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGATTAC--CA 1137s CACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAA 1137s Processing line... 1137s GGGCTGAATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCACGTGGGGTGGATACCCAAAACGCCGAAGTTAGAGCTCGCAGCGCGAAAGAGGGAGGGGTATGGTGA--------G 1137s GGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAACGCNGAAATTAGAGCTCGCAGCGCGTAANAGGGNGGGGTATGGTGAGGGTCGAGG 1137s Processing line... 1137s --- Summary --- 1137s Read 1 reference strings 1137s Checked 85 alignments, 0 edits 1137s --------------- 1137s PASSED 1137s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1138s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 1138s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1138s 70 reads; of these: 1138s 70 (100.00%) were unpaired; of these: 1138s 37 (52.86%) aligned 0 times 1138s 8 (11.43%) aligned exactly 1 time 1138s 25 (35.71%) aligned >1 times 1138s 47.14% overall alignment rate 1138s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1138s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1138s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1138s Flattened IUPAC characters 1138s Mutating sequence Sim.pm.1 1138s Introducing 5 SNPs, 2/0 ref/read gaps, and 0 rearrangements 1138s Finished SNPs 1138s Finished ref gaps 1138s Finished read gaps 1138s Mutating sequence Sim.pm.2 1138s Introducing 15 SNPs, 2/0 ref/read gaps, and 0 rearrangements 1138s Finished SNPs 1138s Finished ref gaps 1138s Finished read gaps 1138s Mutated reference genome to subject genome 1138s SNPs introduced: 20 1138s Reference gaps introduced: 4 1138s Read gaps introduced: 0 1138s Rearrangements introduced: 0 1138s Created read sampler 1138s Sampling 26 reads 1138s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1138s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1138s parsing sequence Sim.pm.1... 1138s parsing sequence Sim.pm.2... 1138s Parsed 269 reference bases 1138s *** Run 34 of 100 1138s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 2 --score-min L,8.72328127011606,8.78071618935134 --n-ceil 0.222181329683127,0.587196661118286 --large-index --ma 14.6925361127898 --mp 3.02207617968157,1.01622207201034 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1138s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1138s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 1138s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1138s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 1138s Warning: skipping mate #2 of read '17' because it was < 2 characters long 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1138s 26 reads; of these: 1138s 26 (100.00%) were paired; of these: 1138s 24 (92.31%) aligned concordantly 0 times 1138s 0 (0.00%) aligned concordantly exactly 1 time 1138s 2 (7.69%) aligned concordantly >1 times 1138s ---- 1138s 24 pairs aligned concordantly 0 times; of these: 1138s 0 (0.00%) aligned discordantly 1 time 1138s ---- 1138s 24 pairs aligned 0 times concordantly or discordantly; of these: 1138s 48 mates make up the pairs; of these: 1138s 40 (83.33%) aligned 0 times 1138s 1 (2.08%) aligned exactly 1 time 1138s 7 (14.58%) aligned >1 times 1138s 23.08% overall alignment rate 1138s Read 50 alignments... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s ATT 1138s ATT 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s GCCTGTCACATCGAG 1138s GCCTGTCACATCGAG 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s AGAACACGAG 1138s AGAACACGAG 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s GAGATGGACCACCTC 1138s GAGATGGACCACCTC 1138s Processing line... 1138s Processing line... 1138s AGATGG 1138s AGATGG 1138s Processing line... 1138s Processing line... 1138s AGCCTGTCACA 1138s AGCCTGTCACA 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s GT 1138s GT 1138s Processing line... 1138s CATCGAGATGGACCACCTCG 1138s CATCGAGATGGACCACCTCG 1138s Processing line... 1138s GAGCCTGTCACAT 1138s GAGCCTGTCACAT 1138s Processing line... 1138s Processing line... 1138s CGAGATGG 1138s CGAGATGG 1138s Processing line... 1138s GAA 1138s GAA 1138s Processing line... 1138s AAATTAGAG 1138s AAATTAGAG 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s Processing line... 1138s --- Summary --- 1138s Read 1 reference strings 1138s Checked 12 alignments, 0 edits 1138s --------------- 1138s PASSED 1138s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1138s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 2 --score-min L,8.72328127011606,8.78071618935134 --n-ceil 0.222181329683127,0.587196661118286 --large-index --ma 14.6925361127898 --mp 3.02207617968157,1.01622207201034 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1138s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1138s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 1138s Warning: skipping mate #2 of read '17' because it was < 2 characters long 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1138s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 1138s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1138s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1138s 26 reads; of these: 1138s 26 (100.00%) were paired; of these: 1138s 24 (92.31%) aligned concordantly 0 times 1138s 0 (0.00%) aligned concordantly exactly 1 time 1138s 2 (7.69%) aligned concordantly >1 times 1138s ---- 1138s 24 pairs aligned concordantly 0 times; of these: 1138s 0 (0.00%) aligned discordantly 1 time 1138s ---- 1138s 24 pairs aligned 0 times concordantly or discordantly; of these: 1138s 48 mates make up the pairs; of these: 1138s 40 (83.33%) aligned 0 times 1138s 1 (2.08%) aligned exactly 1 time 1138s 7 (14.58%) aligned >1 times 1138s 23.08% overall alignment rate 1138s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1138s Flattened IUPAC characters 1138s Mutating sequence Sim.pm.2 1138s Introducing 14 SNPs, 2/3 ref/read gaps, and 1 rearrangements 1138s Finished SNPs 1138s Finished ref gaps 1138s Finished read gaps 1138s Mutating sequence Sim.pm.1 1138s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1138s Finished SNPs 1138s Finished ref gaps 1138s Finished read gaps 1138s Mutated reference genome to subject genome 1138s SNPs introduced: 17 1138s Reference gaps introduced: 2 1138s Read gaps introduced: 3 1138s Rearrangements introduced: 1 1138s Created read sampler 1138s Sampling 74 reads 1138s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1138s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1138s parsing sequence Sim.pm.1... 1138s parsing sequence Sim.pm.2... 1138s Parsed 269 reference bases 1138s *** Run 35 of 100 1138s /usr/bin/bowtie2 --cp-min 6 --np 7 -N 0 -L20 --cp-ival 1 --mp 8.1681376170794,6.56945812581291 -a --trim5 2 --local --large-index --score-min L,7.60513539725752,5.39043001606434 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1139s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1139s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1139s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1139s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1139s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1139s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1139s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 1139s Warning: skipping mate #2 of read '55' because it was < 2 characters long 1139s Read 50 alignments... 1139s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 1139s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1139s Read 100 alignments... 1139s 74 reads; of these: 1139s 71 (95.95%) were paired; of these: 1139s 71 (100.00%) aligned concordantly 0 times 1139s 0 (0.00%) aligned concordantly exactly 1 time 1139s 0 (0.00%) aligned concordantly >1 times 1139s ---- 1139s 71 pairs aligned concordantly 0 times; of these: 1139s 0 (0.00%) aligned discordantly 1 time 1139s ---- 1139s 71 pairs aligned 0 times concordantly or discordantly; of these: 1139s 142 mates make up the pairs; of these: 1139s 142 (100.00%) aligned 0 times 1139s 0 (0.00%) aligned exactly 1 time 1139s 0 (0.00%) aligned >1 times 1139s 3 (4.05%) were unpaired; of these: 1139s 3 (100.00%) aligned 0 times 1139s 0 (0.00%) aligned exactly 1 time 1139s 0 (0.00%) aligned >1 times 1139s 0.00% overall alignment rate 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s Processing line... 1139s --- Summary --- 1139s Read 1 reference strings 1139s Checked 0 alignments, 0 edits 1139s --------------- 1139s PASSED 1139s ALSO checking that bowtie2 and bowtie2-align match up 1139s /usr/bin/bowtie2 --cp-min 6 --np 7 -N 0 -L20 --cp-ival 1 --mp 8.1681376170794,6.56945812581291 -a --trim5 2 --local --large-index --score-min L,7.60513539725752,5.39043001606434 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1139s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1139s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1139s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1139s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1139s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1139s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1139s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 1139s Warning: skipping mate #2 of read '55' because it was < 2 characters long 1139s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 1139s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1139s 74 reads; of these: 1139s 71 (95.95%) were paired; of these: 1139s 71 (100.00%) aligned concordantly 0 times 1139s 0 (0.00%) aligned concordantly exactly 1 time 1139s 0 (0.00%) aligned concordantly >1 times 1139s ---- 1139s 71 pairs aligned concordantly 0 times; of these: 1139s 0 (0.00%) aligned discordantly 1 time 1139s ---- 1139s 71 pairs aligned 0 times concordantly or discordantly; of these: 1139s 142 mates make up the pairs; of these: 1139s 142 (100.00%) aligned 0 times 1139s 0 (0.00%) aligned exactly 1 time 1139s 0 (0.00%) aligned >1 times 1139s 3 (4.05%) were unpaired; of these: 1139s 3 (100.00%) aligned 0 times 1139s 0 (0.00%) aligned exactly 1 time 1139s 0 (0.00%) aligned >1 times 1139s 0.00% overall alignment rate 1139s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1139s /usr/bin/bowtie2 --cp-min 6 --np 7 -N 0 -L20 --cp-ival 1 --mp 8.1681376170794,6.56945812581291 -a --trim5 2 --local --large-index --score-min L,7.60513539725752,5.39043001606434 -r -p 2 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1139s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1139s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1139s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1139s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1139s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1139s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1139s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1139s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 1139s Warning: skipping mate #2 of read '55' because it was < 2 characters long 1139s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 1139s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1139s 74 reads; of these: 1139s 71 (95.95%) were paired; of these: 1139s 71 (100.00%) aligned concordantly 0 times 1139s 0 (0.00%) aligned concordantly exactly 1 time 1139s 0 (0.00%) aligned concordantly >1 times 1139s ---- 1139s 71 pairs aligned concordantly 0 times; of these: 1139s 0 (0.00%) aligned discordantly 1 time 1139s ---- 1139s 71 pairs aligned 0 times concordantly or discordantly; of these: 1139s 142 mates make up the pairs; of these: 1139s 142 (100.00%) aligned 0 times 1139s 0 (0.00%) aligned exactly 1 time 1139s 0 (0.00%) aligned >1 times 1139s 3 (4.05%) were unpaired; of these: 1139s 3 (100.00%) aligned 0 times 1139s 0 (0.00%) aligned exactly 1 time 1139s 0 (0.00%) aligned >1 times 1139s 0.00% overall alignment rate 1139s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1139s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1139s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1139s Flattened IUPAC characters 1139s Mutating sequence Sim.pm.1 1139s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1139s Finished SNPs 1139s Finished ref gaps 1139s Finished read gaps 1139s Mutating sequence Sim.pm.2 1139s Introducing 3 SNPs, 0/1 ref/read gaps, and 2 rearrangements 1139s Finished SNPs 1139s Finished ref gaps 1139s Finished read gaps 1139s Mutated reference genome to subject genome 1139s SNPs introduced: 6 1139s Reference gaps introduced: 0 1139s Read gaps introduced: 1 1139s Rearrangements introduced: 2 1139s Created read sampler 1139s Sampling 72 reads 1139s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1139s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1139s parsing sequence Sim.pm.1... 1139s parsing sequence Sim.pm.2... 1139s Parsed 269 reference bases 1139s *** Run 36 of 100 1139s /usr/bin/bowtie2 --gbar 11 --score-min L,3.08734475887581,4.79626570208119 --trim5 5 --rfg 23.4610083383442,17.3448420494383 --large-index --trim3 9 --mp 9.08676167315559,9.07341856706915 --local --mm --cp-ival 3 --cp-min 8 -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw 1140s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '1' because it was < 2 characters long 1140s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '5' because it was < 2 characters long 1140s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '8' because it was < 2 characters long 1140s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '12' because it was < 2 characters long 1140s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '14' because it was < 2 characters long 1140s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '16' because it was < 2 characters long 1140s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '18' because it was < 2 characters long 1140s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '28' because it was < 2 characters long 1140s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '31' because it was < 2 characters long 1140s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '35' because it was < 2 characters long 1140s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '38' because it was < 2 characters long 1140s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 1140s Warning: skipping read '40' because it was < 2 characters long 1140s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '46' because it was < 2 characters long 1140s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '47' because it was < 2 characters long 1140s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '48' because it was < 2 characters long 1140s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '50' because it was < 2 characters long 1140s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '53' because it was < 2 characters long 1140s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '54' because it was < 2 characters long 1140s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '56' because it was < 2 characters long 1140s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 1140s Warning: skipping read '59' because it was < 2 characters long 1140s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '60' because it was < 2 characters long 1140s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '62' because it was < 2 characters long 1140s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '67' because it was < 2 characters long 1140s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '70' because it was < 2 characters long 1140s 72 reads; of these: 1140s 72 (100.00%) were unpaired; of these: 1140s 72 (100.00%) aligned 0 times 1140s 0 (0.00%) aligned exactly 1 time 1140s 0 (0.00%) aligned >1 times 1140s 0.00% overall alignment rate 1140s Read 50 alignments... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s --- Summary --- 1140s Read 1 reference strings 1140s Checked 0 alignments, 0 edits 1140s --------------- 1140s PASSED 1140s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1140s /usr/bin/bowtie2 --gbar 11 --score-min L,3.08734475887581,4.79626570208119 --trim5 5 --rfg 23.4610083383442,17.3448420494383 --large-index --trim3 9 --mp 9.08676167315559,9.07341856706915 --local --mm --cp-ival 3 --cp-min 8 -r -p 2 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1140s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '1' because it was < 2 characters long 1140s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '5' because it was < 2 characters long 1140s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '8' because it was < 2 characters long 1140s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '12' because it was < 2 characters long 1140s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '14' because it was < 2 characters long 1140s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '16' because it was < 2 characters long 1140s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '18' because it was < 2 characters long 1140s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '28' because it was < 2 characters long 1140s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '31' because it was < 2 characters long 1140s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '35' because it was < 2 characters long 1140s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '38' because it was < 2 characters long 1140s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 1140s Warning: skipping read '40' because it was < 2 characters long 1140s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '46' because it was < 2 characters long 1140s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '47' because it was < 2 characters long 1140s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '48' because it was < 2 characters long 1140s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '50' because it was < 2 characters long 1140s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '53' because it was < 2 characters long 1140s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '54' because it was < 2 characters long 1140s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '56' because it was < 2 characters long 1140s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 1140s Warning: skipping read '59' because it was < 2 characters long 1140s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '60' because it was < 2 characters long 1140s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '62' because it was < 2 characters long 1140s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '67' because it was < 2 characters long 1140s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 1140s Warning: skipping read '70' because it was < 2 characters long 1140s 72 reads; of these: 1140s 72 (100.00%) were unpaired; of these: 1140s 72 (100.00%) aligned 0 times 1140s 0 (0.00%) aligned exactly 1 time 1140s 0 (0.00%) aligned >1 times 1140s 0.00% overall alignment rate 1140s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1140s Flattened IUPAC characters 1140s Mutating sequence Sim.pm.1 1140s Introducing 3 SNPs, 2/1 ref/read gaps, and 0 rearrangements 1140s Finished SNPs 1140s Finished ref gaps 1140s Finished read gaps 1140s Mutating sequence Sim.pm.2 1140s Introducing 5 SNPs, 1/4 ref/read gaps, and 0 rearrangements 1140s Finished SNPs 1140s Finished ref gaps 1140s Finished read gaps 1140s Mutated reference genome to subject genome 1140s SNPs introduced: 8 1140s Reference gaps introduced: 3 1140s Read gaps introduced: 5 1140s Rearrangements introduced: 0 1140s Created read sampler 1140s Sampling 19 reads 1140s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1140s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1140s parsing sequence Sim.pm.1... 1140s parsing sequence Sim.pm.2... 1140s Parsed 269 reference bases 1140s *** Run 37 of 100 1140s /usr/bin/bowtie2 --cp-min 6 --cp-ival 1 --mm --trim3 7 --mp 8.58564535611302,1.03084398835047 --local --large-index -M 2 --nofw --np 5 -N 0 -D 45 --rfg 37.2060716676135 --score-min L,6.92575944107471,2.15184625047582 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1140s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1140s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 1140s Warning: skipping read '6' because it was < 2 characters long 1140s 19 reads; of these: 1140s 19 (100.00%) were unpaired; of these: 1140s 19 (100.00%) aligned 0 times 1140s 0 (0.00%) aligned exactly 1 time 1140s 0 (0.00%) aligned >1 times 1140s 0.00% overall alignment rate 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s --- Summary --- 1140s Read 1 reference strings 1140s Checked 0 alignments, 0 edits 1140s --------------- 1140s PASSED 1140s Flattened IUPAC characters 1140s Mutating sequence Sim.pm.1 1140s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1140s Finished SNPs 1140s Finished ref gaps 1140s Finished read gaps 1140s Mutating sequence Sim.pm.2 1140s Introducing 18 SNPs, 2/0 ref/read gaps, and 2 rearrangements 1140s Finished SNPs 1140s Finished ref gaps 1140s Finished read gaps 1140s Mutated reference genome to subject genome 1140s SNPs introduced: 22 1140s Reference gaps introduced: 2 1140s Read gaps introduced: 0 1140s Rearrangements introduced: 3 1140s Created read sampler 1140s Sampling 65 reads 1140s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1140s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1140s parsing sequence Sim.pm.1... 1140s parsing sequence Sim.pm.2... 1140s Parsed 269 reference bases 1140s *** Run 38 of 100 1140s /usr/bin/bowtie2 --rfg 33.2773332873235 -i S,0.179506737859022 --score-min L,9.32105455514492,9.65913414444141 --np 2 --local --rdg 17.2861203063839,12.5850442893471 --trim3 0 -k 3 --large-index --cp-min 2 --mm --cp-ival 2 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1140s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 1140s Warning: skipping read '16' because it was < 2 characters long 1140s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 1140s Warning: skipping read '64' because it was < 2 characters long 1140s 65 reads; of these: 1140s 65 (100.00%) were unpaired; of these: 1140s 65 (100.00%) aligned 0 times 1140s 0 (0.00%) aligned exactly 1 time 1140s 0 (0.00%) aligned >1 times 1140s 0.00% overall alignment rate 1140s /usr/bin/bowtie2 --rfg 33.2773332873235 -i S,0.179506737859022 --score-min L,9.32105455514492,9.65913414444141 --np 2 --local --rdg 17.2861203063839,12.5850442893471 --trim3 0 -k 3 --large-index --cp-min 2 --mm --cp-ival 2 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1140s Read 50 alignments... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s Processing line... 1140s --- Summary --- 1140s Read 1 reference strings 1140s Checked 0 alignments, 0 edits 1140s --------------- 1140s PASSED 1140s ALSO checking that bowtie2 and bowtie2-align match up 1140s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 1140s Warning: skipping read '16' because it was < 2 characters long 1140s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 1140s Warning: skipping read '64' because it was < 2 characters long 1140s 65 reads; of these: 1140s 65 (100.00%) were unpaired; of these: 1140s 65 (100.00%) aligned 0 times 1140s 0 (0.00%) aligned exactly 1 time 1140s 0 (0.00%) aligned >1 times 1140s 0.00% overall alignment rate 1140s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1140s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1140s /usr/bin/bowtie2 --rfg 33.2773332873235 -i S,0.179506737859022 --score-min L,9.32105455514492,9.65913414444141 --np 2 --local --rdg 17.2861203063839,12.5850442893471 --trim3 0 -k 3 --large-index --cp-min 2 --mm --cp-ival 2 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1141s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 1141s Warning: skipping read '16' because it was < 2 characters long 1141s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 1141s Warning: skipping read '64' because it was < 2 characters long 1141s 65 reads; of these: 1141s 65 (100.00%) were unpaired; of these: 1141s 65 (100.00%) aligned 0 times 1141s 0 (0.00%) aligned exactly 1 time 1141s 0 (0.00%) aligned >1 times 1141s 0.00% overall alignment rate 1141s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1141s Flattened IUPAC characters 1141s Mutating sequence Sim.pm.2 1141s Introducing 11 SNPs, 1/2 ref/read gaps, and 1 rearrangements 1141s Finished SNPs 1141s Finished ref gaps 1141s Finished read gaps 1141s Mutating sequence Sim.pm.1 1141s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1141s Finished SNPs 1141s Finished ref gaps 1141s Finished read gaps 1141s Mutated reference genome to subject genome 1141s SNPs introduced: 11 1141s Reference gaps introduced: 1 1141s Read gaps introduced: 2 1141s Rearrangements introduced: 2 1141s Created read sampler 1141s Sampling 98 reads 1141s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1141s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1141s parsing sequence Sim.pm.1... 1141s *** Run 39 of 100 1141s /usr/bin/bowtie2 --cp-ival 2 -N 1 -L18 --cp-min 3 --score-min L,8.07704222646942,3.0168005132247 --large-index --ma 24.9949408129649 --n-ceil 0.299313072553655,0.981822502778337 -i C,3.21884586410685 --trim5 6 --rdg 47.8662594676167 --mp 7.12163023899243,5.39870207891319 --trim3 6 --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1141s parsing sequence Sim.pm.2... 1141s Parsed 269 reference bases 1141s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1141s 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 1141s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1141s 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 1141s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 1141s 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 1141s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 1141s 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 1141s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1141s 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 1141s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 1141s 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 1141s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1141s 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 1141s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1141s 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 1141s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1141s 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 1141s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (1) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (1) 1141s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 98 reads; of these: 1141s 98 (100.00%) were unpaired; of these: 1141s 84 (85.71%) aligned 0 times 1141s 4 (4.08%) aligned exactly 1 time 1141s 10 (10.20%) aligned >1 times 1141s 14.29% overall alignment rate 1141s Read 50 alignments... 1141s Read 100 alignments... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s ATG 1141s ATG 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s CGCAGCGCGTAA 1141s CGCAGCGCGTAA 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s CGCAGCGCGTAA 1141s CGCAGCGCGTAA 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s GATGGACCACCTCGTG 1141s GATGGACCACCTCGTG 1141s Processing line... 1141s Processing line... 1141s TCACATCGAGATGGACC 1141s TCACATCGAGATGGACC 1141s Processing line... 1141s AG 1141s AG 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s GATGGACCA 1141s GATGGACCA 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s GTGGCTGAG 1141s GTGGCTGAG 1141s Processing line... 1141s CGCAGCGCGTAA 1141s CGCAGCGCGTAA 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s GAGCCTGTCACATCG 1141s GAGCCTGTCACATCG 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s GTAGA 1141s GTAGA 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s AGAACACGAGCCTGTCAC 1141s AGAACACGAGCCTGTCAC 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s AGAT 1141s AGAT 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s CA 1141s CA 1141s Processing line... 1141s Processing line... 1141s --- Summary --- 1141s Read 1 reference strings 1141s Checked 14 alignments, 0 edits 1141s --------------- 1141s PASSED 1141s Flattened IUPAC characters 1141s Mutating sequence Sim.pm.1 1141s Introducing 4 SNPs, 2/2 ref/read gaps, and 0 rearrangements 1141s Finished SNPs 1141s Finished ref gaps 1141s Finished read gaps 1141s Mutating sequence Sim.pm.2 1141s Introducing 2 SNPs, 1/2 ref/read gaps, and 1 rearrangements 1141s Finished SNPs 1141s Finished ref gaps 1141s Finished read gaps 1141s Mutated reference genome to subject genome 1141s SNPs introduced: 6 1141s Reference gaps introduced: 3 1141s Read gaps introduced: 4 1141s Rearrangements introduced: 1 1141s Created read sampler 1141s Sampling 64 reads 1141s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1141s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1141s parsing sequence Sim.pm.1... 1141s parsing sequence Sim.pm.2... 1141s Parsed 269 reference bases 1141s *** Run 40 of 100 1141s /usr/bin/bowtie2 --cp-ival 1 --norc --cp-min 2 --score-min L,5.09786405382606,6.89462271055343 --large-index --ma 35.7377339600154 -i S,2.43838755705531,4.21117503286799 --trim5 4 --rdg 42.5701722500216,7.48440367690023 --mp 7.28236947022444,2.4645401805108 --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1141s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 1141s 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 1141s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1141s 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 1141s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 1141s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 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 1141s 64 reads; of these: 1141s 64 (100.00%) were unpaired; of these: 1141s 54 (84.38%) aligned 0 times 1141s 1 (1.56%) aligned exactly 1 time 1141s 9 (14.06%) aligned >1 times 1141s 15.62% overall alignment rate 1141s Read 50 alignments... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s TA 1141s TA 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s GG 1141s GG 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s AGCCT 1141s AGCCT 1141s Processing line... 1141s GAGATGGACCACCTCGTGG 1141s GAGATGGACCACCTCGTGG 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s Processing line... 1141s ACGAGCCTGTCACATCGAGATGGA 1141s ACGAGCCTGTCACATCGAGATGGA 1141s Processing line... 1141s CGCA 1141s CGCA 1141s Processing line... 1141s AGCCT 1141s AGCCT 1141s Processing line... 1141s Processing line... 1142s *** Run 41 of 100 1142s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --rdg 13.343776478535,2.94850307312923 --mp 5.9395271566975,5.88114901767004 --local -M 6 --large-index --rfg 7.29172975141417,12.8978497042867 --score-min L,9.5342828670582,5.57773317168808 -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s GAGCCTGTCACATCGAGATGG 1142s GAGCCTGTCACATCGAGATGG 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s AGTAGAA 1142s AGTAGAA 1142s Processing line... 1142s CACATCGAGATGGACCAC 1142s CACATCGAGATGGACCAC 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s --- Summary --- 1142s Read 1 reference strings 1142s Checked 10 alignments, 0 edits 1142s --------------- 1142s PASSED 1142s Flattened IUPAC characters 1142s Mutating sequence Sim.pm.1 1142s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1142s Finished SNPs 1142s Finished ref gaps 1142s Finished read gaps 1142s Mutating sequence Sim.pm.2 1142s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1142s Finished SNPs 1142s Finished ref gaps 1142s Finished read gaps 1142s Mutated reference genome to subject genome 1142s SNPs introduced: 5 1142s Reference gaps introduced: 1 1142s Read gaps introduced: 1 1142s Rearrangements introduced: 0 1142s Created read sampler 1142s Sampling 173 reads 1142s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1142s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1142s parsing sequence Sim.pm.1... 1142s parsing sequence Sim.pm.2... 1142s Parsed 269 reference bases 1142s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1142s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '44' because it was < 2 characters long 1142s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '45' because it was < 2 characters long 1142s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '54' because it was < 2 characters long 1142s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '82' because it was < 2 characters long 1142s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '95' because it was < 2 characters long 1142s Warning: skipping read '128' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '128' because it was < 2 characters long 1142s Read 50 alignments... 1142s Read 100 alignments... 1142s 173 reads; of these: 1142s 173 (100.00%) were unpaired; of these: 1142s 173 (100.00%) aligned 0 times 1142s 0 (0.00%) aligned exactly 1 time 1142s 0 (0.00%) aligned >1 times 1142s 0.00% overall alignment rate 1142s Read 150 alignments... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s Processing line... 1142s --- Summary --- 1142s Read 1 reference strings 1142s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --rdg 13.343776478535,2.94850307312923 --mp 5.9395271566975,5.88114901767004 --local -M 6 --large-index --rfg 7.29172975141417,12.8978497042867 --score-min L,9.5342828670582,5.57773317168808 -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1142s Checked 0 alignments, 0 edits 1142s --------------- 1142s PASSED 1142s ALSO checking that bowtie2 and bowtie2-align match up 1142s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1142s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '44' because it was < 2 characters long 1142s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '45' because it was < 2 characters long 1142s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '54' because it was < 2 characters long 1142s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '82' because it was < 2 characters long 1142s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '95' because it was < 2 characters long 1142s Warning: skipping read '128' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '128' because it was < 2 characters long 1142s 173 reads; of these: 1142s 173 (100.00%) were unpaired; of these: 1142s 173 (100.00%) aligned 0 times 1142s 0 (0.00%) aligned exactly 1 time 1142s 0 (0.00%) aligned >1 times 1142s 0.00% overall alignment rate 1142s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1142s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1142s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --rdg 13.343776478535,2.94850307312923 --mp 5.9395271566975,5.88114901767004 --local -M 6 --large-index --rfg 7.29172975141417,12.8978497042867 --score-min L,9.5342828670582,5.57773317168808 -r -p 2 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1142s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1142s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '54' because it was < 2 characters long 1142s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '44' because it was < 2 characters long 1142s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '45' because it was < 2 characters long 1142s Warning: skipping read '128' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '128' because it was < 2 characters long 1142s Warning: skipping read '82' because it was < 2 characters long 1142s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 1142s Warning: skipping read '95' because it was < 2 characters long 1142s 173 reads; of these: 1142s 173 (100.00%) were unpaired; of these: 1142s 173 (100.00%) aligned 0 times 1142s 0 (0.00%) aligned exactly 1 time 1142s 0 (0.00%) aligned >1 times 1142s 0.00% overall alignment rate 1142s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1143s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1143s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1143s Flattened IUPAC characters 1143s Mutating sequence Sim.pm.1 1143s Introducing 2 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1143s Finished SNPs 1143s Finished ref gaps 1143s Finished read gaps 1143s Mutating sequence Sim.pm.2 1143s Introducing 10 SNPs, 2/1 ref/read gaps, and 1 rearrangements 1143s Finished SNPs 1143s Finished ref gaps 1143s Finished read gaps 1143s Mutated reference genome to subject genome 1143s SNPs introduced: 12 1143s Reference gaps introduced: 2 1143s Read gaps introduced: 1 1143s Rearrangements introduced: 3 1143s Created read sampler 1143s Sampling 100 reads 1143s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1143s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1143s parsing sequence Sim.pm.1... 1143s parsing sequence Sim.pm.2... 1143s Parsed 269 reference bases 1143s *** Run 42 of 100 1143s /usr/bin/bowtie2 --rfg 17.7119208790889 --mp 7.09297855845801,3.62593950852978 --rdg 36.4795408820552,9.97262055458163 --score-min L,5.51509484219507,6.96025343407949 --large-index --cp-min 4 --cp-ival 1 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1143s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1143s 100 reads; of these: 1143s 100 (100.00%) were unpaired; of these: 1143s 85 (85.00%) aligned 0 times 1143s 3 (3.00%) aligned exactly 1 time 1143s 12 (12.00%) aligned >1 times 1143s 15.00% overall alignment rate 1143s Read 50 alignments... 1143s Read 100 alignments... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s CGAG 1143s CGAG 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s GAACACGAGC 1143s GAACACGAGC 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s TAGAGCTC 1143s TAGAGCTC 1143s Processing line... 1143s Processing line... 1143s TG 1143s TG 1143s Processing line... 1143s AGTAGAACACGAGCCTGTCACATCGAGATGGAC 1143s AGTAGAACACGAGCCTGTCACATCGAGATGGAC 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s GTAGAACACGAGCCTG 1143s GTAGAACACGAGCCTG 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s ATGGACCAC 1143s ATGGACCAC 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s AG 1143s AG 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s AGCTCGCAGCGCGT 1143s AGCTCGCAGCGCGT 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s CGC 1143s CGC 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s GGTGAGGGTCGA 1143s GGTGAGGGTCGA 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s ACACGAGCCTGTCACATCGAGATGGACCACCTC 1143s ACACGAGCCTGTCACATCGAGATGGACCACCTC 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s TA 1143s TA 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s TCG 1143s TCG 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s AACACGAGCCTGTCAC 1143s AACACGAGCCTGTCAC 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s --- Summary --- 1143s Read 1 reference strings 1143s Checked 15 alignments, 0 edits 1143s --------------- 1143s PASSED 1143s Flattened IUPAC characters 1143s Mutating sequence Sim.pm.2 1143s Introducing 7 SNPs, 0/3 ref/read gaps, and 2 rearrangements 1143s Finished SNPs 1143s Finished ref gaps 1143s Finished read gaps 1143s Mutating sequence Sim.pm.1 1143s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1143s Finished SNPs 1143s Finished ref gaps 1143s Finished read gaps 1143s Mutated reference genome to subject genome 1143s SNPs introduced: 7 1143s Reference gaps introduced: 0 1143s Read gaps introduced: 3 1143s Rearrangements introduced: 2 1143s Created read sampler 1143s Sampling 130 reads 1143s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1143s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1143s parsing sequence Sim.pm.1... 1143s *** Run 43 of 100 1143s /usr/bin/bowtie2 --mm --cp-ival 2 --cp-min 2 --large-index --trim3 4 --local --norc --score-min L,9.71874615414693,9.9484182142725 --trim5 6 --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1143s parsing sequence Sim.pm.2... 1143s Parsed 269 reference bases 1143s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 1143s Read 50 alignments... 1143s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_126_126_1/1' because length (1) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 1143s Read 100 alignments... 1143s 130 reads; of these: 1143s 130 (100.00%) were unpaired; of these: 1143s 130 (100.00%) aligned 0 times 1143s 0 (0.00%) aligned exactly 1 time 1143s 0 (0.00%) aligned >1 times 1143s 0.00% overall alignment rate 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s Processing line... 1143s --- Summary --- 1143s Read 1 reference strings 1143s Checked 0 alignments, 0 edits 1143s --------------- 1143s PASSED 1143s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1143s /usr/bin/bowtie2 --mm --cp-ival 2 --cp-min 2 --large-index --trim3 4 --local --norc --score-min L,9.71874615414693,9.9484182142725 --trim5 6 --qseq -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1143s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_126_126_1/1' because length (1) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 1143s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 1143s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 1143s 130 reads; of these: 1143s 130 (100.00%) were unpaired; of these: 1143s 130 (100.00%) aligned 0 times 1143s 0 (0.00%) aligned exactly 1 time 1143s 0 (0.00%) aligned >1 times 1143s 0.00% overall alignment rate 1143s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1143s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1143s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1143s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1143s /usr/bin/bowtie2 --mm --cp-ival 2 --cp-min 2 --large-index --trim3 4 --local --norc --score-min L,9.71874615414693,9.9484182142725 --trim5 6 --qseq -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1144s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 1144s Warning: skipping read 'R_1_1_1_126_126_1/1' because length (1) <= # seed mismatches (0) 1144s Warning: skipping read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 1144s 130 reads; of these: 1144s 130 (100.00%) were unpaired; of these: 1144s 130 (100.00%) aligned 0 times 1144s 0 (0.00%) aligned exactly 1 time 1144s 0 (0.00%) aligned >1 times 1144s 0.00% overall alignment rate 1144s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1144s Flattened IUPAC characters 1144s Mutating sequence Sim.pm.1 1144s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1144s Finished SNPs 1144s Finished ref gaps 1144s Finished read gaps 1144s Mutating sequence Sim.pm.2 1144s Introducing 0 SNPs, 4/0 ref/read gaps, and 0 rearrangements 1144s Finished SNPs 1144s Finished ref gaps 1144s Finished read gaps 1144s Mutated reference genome to subject genome 1144s SNPs introduced: 7 1144s Reference gaps introduced: 5 1144s Read gaps introduced: 0 1144s Rearrangements introduced: 0 1144s Created read sampler 1144s Sampling 23 reads 1144s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1144s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1144s parsing sequence Sim.pm.1... 1144s parsing sequence Sim.pm.2... 1144s Parsed 269 reference bases 1144s *** Run 44 of 100 1144s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --local --rdg 12.5832535338479,9.15048899538422 --mp 6.35749704874458,2.48065905871616 --large-index -M 5 -D 13 --trim5 7 --gbar 4 --score-min L,9.27295159883839,2.33182814866556 --n-ceil 1.49361787059229,0.295282953464916 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1144s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1144s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '1' because it was < 2 characters long 1144s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '6' because it was < 2 characters long 1144s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '8' because it was < 2 characters long 1144s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '11' because it was < 2 characters long 1144s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 1144s Warning: skipping read '15' because it was < 2 characters long 1144s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '17' because it was < 2 characters long 1144s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '20' because it was < 2 characters long 1144s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '23' because it was < 2 characters long 1144s 23 reads; of these: 1144s 23 (100.00%) were unpaired; of these: 1144s 23 (100.00%) aligned 0 times 1144s 0 (0.00%) aligned exactly 1 time 1144s 0 (0.00%) aligned >1 times 1144s 0.00% overall alignment rate 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s --- Summary --- 1144s Read 1 reference strings 1144s Checked 0 alignments, 0 edits 1144s --------------- 1144s PASSED 1144s Flattened IUPAC characters 1144s Mutating sequence Sim.pm.1 1144s Introducing 11 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1144s Finished SNPs 1144s Finished ref gaps 1144s Finished read gaps 1144s Mutating sequence Sim.pm.2 1144s Introducing 4 SNPs, 0/1 ref/read gaps, and 3 rearrangements 1144s Finished SNPs 1144s Finished ref gaps 1144s Finished read gaps 1144s Mutated reference genome to subject genome 1144s SNPs introduced: 15 1144s Reference gaps introduced: 1 1144s Read gaps introduced: 1 1144s Rearrangements introduced: 3 1144s Created read sampler 1144s Sampling 106 reads 1144s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1144s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1144s *** Run 45 of 100 1144s /usr/bin/bowtie2 --cp-min 2 --cp-ival 2 --mp 9.29315724173485,1.72165988913788 --trim5 6 --score-min L,2.24538589215735,4.94900943975235 --gbar 4 --large-index -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw 1144s parsing sequence Sim.pm.1... 1144s parsing sequence Sim.pm.2... 1144s Parsed 269 reference bases 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1144s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '0' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1144s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '2' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1144s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '10' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1144s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '18' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1144s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '34' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1144s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 1144s Warning: skipping read '41' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1144s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '46' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1144s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '51' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1144s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '54' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1144s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '62' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1144s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 1144s Warning: skipping read '64' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1144s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '69' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1144s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '71' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1144s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '77' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1144s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '78' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1144s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '95' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1144s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '96' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1144s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '100' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1144s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1144s Warning: skipping read '104' because it was < 2 characters long 1144s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1144s 106 reads; of these: 1144s 106 (100.00%) were unpaired; of these: 1144s 92 (86.79%) aligned 0 times 1144s 3 (2.83%) aligned exactly 1 time 1144s 11 (10.38%) aligned >1 times 1144s 13.21% overall alignment rate 1144s Read 50 alignments... 1144s Read 100 alignments... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s CCT 1144s CCT 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s GAACACGAGCCTGT 1144s GAACACGAGCCTGT 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s GGA 1144s GGA 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s AAATTA 1144s AAATTA 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s AATTAGAG 1144s AATTAGAG 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s CATCGAG 1144s CATCGAG 1144s Processing line... 1144s TAGAACACGAGCCTGT 1144s TAGAACACGAGCCTGT 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s ACACGAGCCTGTCAC 1144s ACACGAGCCTGTCAC 1144s Processing line... 1144s GGA 1144s GGA 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s CCACCTCGT 1144s CCACCTCGT 1144s Processing line... 1144s Processing line... 1144s AA 1144s AA 1144s Processing line... 1144s Processing line... 1144s /usr/bin/bowtie2 --cp-min 2 --cp-ival 2 --mp 9.29315724173485,1.72165988913788 --trim5 6 --score-min L,2.24538589215735,4.94900943975235 --gbar 4 --large-index -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1144s Processing line... 1144s Processing line... 1144s CTGAAGTGG 1144s CTGAAGTGG 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s ACCTCGTGGG 1144s ACCTCGTGGG 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s AGATGGACCACCTCG 1144s AGATGGACCACCTCG 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s Processing line... 1144s --- Summary --- 1144s Read 1 reference strings 1144s Checked 14 alignments, 0 edits 1144s --------------- 1144s PASSED 1144s ALSO checking that bowtie2 and bowtie2-align match up 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1145s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '0' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1145s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '2' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1145s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '10' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1145s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '18' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1145s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '34' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1145s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 1145s Warning: skipping read '41' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1145s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '46' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1145s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '51' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1145s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '54' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1145s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '62' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1145s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 1145s Warning: skipping read '64' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1145s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '69' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1145s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '71' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1145s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '77' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1145s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '78' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1145s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '95' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1145s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '96' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1145s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '100' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1145s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '104' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1145s 106 reads; of these: 1145s 106 (100.00%) were unpaired; of these: 1145s 92 (86.79%) aligned 0 times 1145s 3 (2.83%) aligned exactly 1 time 1145s 11 (10.38%) aligned >1 times 1145s 13.21% overall alignment rate 1145s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1145s /usr/bin/bowtie2 --cp-min 2 --cp-ival 2 --mp 9.29315724173485,1.72165988913788 --trim5 6 --score-min L,2.24538589215735,4.94900943975235 --gbar 4 --large-index -r -p 2 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1145s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1145s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '0' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1145s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '2' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1145s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '10' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1145s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '18' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1145s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '51' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1145s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '54' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1145s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '34' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1145s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 1145s Warning: skipping read '41' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1145s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '62' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1145s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 1145s Warning: skipping read '64' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1145s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '69' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1145s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '71' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1145s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '77' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1145s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '78' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1145s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '46' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1145s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '96' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1145s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '100' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1145s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '104' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1145s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '95' because it was < 2 characters long 1145s 106 reads; of these: 1145s 106 (100.00%) were unpaired; of these: 1145s 92 (86.79%) aligned 0 times 1145s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1145s 3 (2.83%) aligned exactly 1 time 1145s 11 (10.38%) aligned >1 times 1145s 13.21% overall alignment rate 1145s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1145s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1145s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1145s /usr/bin/bowtie2 --cp-min 2 --cp-ival 2 --mp 9.29315724173485,1.72165988913788 --trim5 6 --score-min L,2.24538589215735,4.94900943975235 --gbar 4 --large-index -r -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1145s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '0' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1145s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '2' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1145s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '10' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1145s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '34' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1145s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 1145s Warning: skipping read '41' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1145s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '46' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1145s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 1145s Warning: skipping read '64' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1145s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '18' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1145s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '69' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1145s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '71' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1145s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '77' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1145s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '78' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1145s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '96' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1145s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '100' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1145s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '104' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1145s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '51' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1145s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '54' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1145s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '62' because it was < 2 characters long 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1145s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1145s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1145s Warning: skipping read '95' because it was < 2 characters long 1145s 106 reads; of these: 1145s 106 (100.00%) were unpaired; of these: 1145s 92 (86.79%) aligned 0 times 1145s 3 (2.83%) aligned exactly 1 time 1145s 11 (10.38%) aligned >1 times 1145s 13.21% overall alignment rate 1146s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1146s Flattened IUPAC characters 1146s Mutating sequence Sim.pm.1 1146s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1146s Finished SNPs 1146s Finished ref gaps 1146s Finished read gaps 1146s Mutating sequence Sim.pm.2 1146s Introducing 23 SNPs, 4/2 ref/read gaps, and 1 rearrangements 1146s Finished SNPs 1146s Finished ref gaps 1146s Finished read gaps 1146s Mutated reference genome to subject genome 1146s SNPs introduced: 23 1146s Reference gaps introduced: 5 1146s Read gaps introduced: 3 1146s Rearrangements introduced: 1 1146s Created read sampler 1146s Sampling 50 reads 1146s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1146s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1146s parsing sequence Sim.pm.1... 1146s parsing sequence Sim.pm.2... 1146s Parsed 269 reference bases 1146s *** Run 46 of 100 1146s /usr/bin/bowtie2 --np 10 --cp-min 9 --mm -R 2 --cp-ival 2 --rfg 8.81330781110151 --rdg 30.8225369127074 --mp 6.10055009859929,3.11523873628829 --score-min L,1.06653714676185,2.62587903635563 --large-index -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1146s 50 reads; of these: 1146s 50 (100.00%) were unpaired; of these: 1146s 43 (86.00%) aligned 0 times 1146s 1 (2.00%) aligned exactly 1 time 1146s 6 (12.00%) aligned >1 times 1146s 14.00% overall alignment rate 1146s Read 50 alignments... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s CTG 1146s CTG 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s GATA 1146s GATA 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s GATAA 1146s GATAA 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s TAGAGC 1146s TAGAGC 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s ACCACCTCGTGGG 1146s ACCACCTCGTGGG 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s TAGAACACGA 1146s TAGAACACGA 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s Processing line... 1146s ACACGAGCCTGTCAC 1146s ACACGAGCCTGTCAC 1146s --- Summary --- 1146s /usr/bin/bowtie2 --np 10 --cp-min 9 --mm -R 2 --cp-ival 2 --rfg 8.81330781110151 --rdg 30.8225369127074 --mp 6.10055009859929,3.11523873628829 --score-min L,1.06653714676185,2.62587903635563 --large-index -f -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1146s Read 1 reference strings 1146s Checked 7 alignments, 0 edits 1146s --------------- 1146s PASSED 1146s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1146s 50 reads; of these: 1146s 50 (100.00%) were unpaired; of these: 1146s 43 (86.00%) aligned 0 times 1146s 1 (2.00%) aligned exactly 1 time 1146s 6 (12.00%) aligned >1 times 1146s 14.00% overall alignment rate 1146s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1146s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1146s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1146s Flattened IUPAC characters 1146s Mutating sequence Sim.pm.2 1146s Introducing 14 SNPs, 2/4 ref/read gaps, and 3 rearrangements 1146s Finished SNPs 1146s Finished ref gaps 1146s Finished read gaps 1146s Mutating sequence Sim.pm.1 1146s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1146s Finished SNPs 1146s Finished ref gaps 1146s Finished read gaps 1146s Mutated reference genome to subject genome 1146s SNPs introduced: 19 1146s Reference gaps introduced: 3 1146s Read gaps introduced: 4 1146s Rearrangements introduced: 3 1146s Created read sampler 1146s Sampling 171 reads 1146s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1146s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1146s parsing sequence Sim.pm.1... 1146s parsing sequence Sim.pm.2... 1146s Parsed 269 reference bases 1146s *** Run 47 of 100 1146s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 4 --large-index --score-min L,5.57610935390429,7.38388055778567 -a -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1146s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 1146s Warning: skipping mate #2 of read '5' because it was < 2 characters long 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1146s Read 50 alignments... 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1146s Read 100 alignments... 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1146s Read 150 alignments... 1146s Read 200 alignments... 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1146s Warning: skipping mate #1 of read '50' because length (1) <= # seed mismatches (0) 1146s Warning: skipping mate #1 of read '50' because it was < 2 characters long 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1146s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 1146s Warning: skipping mate #2 of read '56' because it was < 2 characters long 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1146s Read 250 alignments... 1146s Read 300 alignments... 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1146s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1147s Warning: skipping mate #1 of read '97' because length (1) <= # seed mismatches (0) 1147s Warning: skipping mate #1 of read '97' because it was < 2 characters long 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1147s Read 350 alignments... 1147s Read 400 alignments... 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1147s Read 450 alignments... 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 1147s Warning: skipping mate #1 of read '137' because length (1) <= # seed mismatches (0) 1147s Warning: skipping mate #1 of read '137' because it was < 2 characters long 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 1147s Warning: skipping mate #2 of read '141' because length (1) <= # seed mismatches (0) 1147s Warning: skipping mate #2 of read '141' because it was < 2 characters long 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 1147s Read 500 alignments... 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 1147s Read 550 alignments... 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 1147s 171 reads; of these: 1147s 171 (100.00%) were paired; of these: 1147s 167 (97.66%) aligned concordantly 0 times 1147s 0 (0.00%) aligned concordantly exactly 1 time 1147s 4 (2.34%) aligned concordantly >1 times 1147s ---- 1147s 167 pairs aligned concordantly 0 times; of these: 1147s 0 (0.00%) aligned discordantly 1 time 1147s ---- 1147s 167 pairs aligned 0 times concordantly or discordantly; of these: 1147s 334 mates make up the pairs; of these: 1147s 276 (82.63%) aligned 0 times 1147s 6 (1.80%) aligned exactly 1 time 1147s 52 (15.57%) aligned >1 times 1147s 19.30% overall alignment rate 1147s Read 600 alignments... 1147s Read 650 alignments... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s ATCGAGATG 1147s ATCGAGATG 1147s Processing line... 1147s ATCGAGATG 1147s ATCGAGATG 1147s Processing line... 1147s ATCGAGATG 1147s ATCGAGATG 1147s Processing line... 1147s CACATCG 1147s CACATCG 1147s Processing line... 1147s CACATCG 1147s CACATCG 1147s Processing line... 1147s CACATCG 1147s CACATCG 1147s Processing line... 1147s GTCACATCGAGATGGACCA 1147s GTCACATCGAGATGGACCA 1147s Processing line... 1147s GTCACATCGAGATGGACCA 1147s GTCACATCGAGATGGACCA 1147s Processing line... 1147s GTCACATCGAGATGGACCA 1147s GTCACATCGAGATGGACCA 1147s Processing line... 1147s Processing line... 1147s AGAGCTCGC 1147s AGAGCTCGC 1147s Processing line... 1147s CTCGT 1147s CTCGT 1147s Processing line... 1147s AGAGCTCGC 1147s AGAGCTCGC 1147s Processing line... 1147s CTCGT 1147s CTCGT 1147s Processing line... 1147s AGAGCTCGC 1147s AGAGCTCGC 1147s Processing line... 1147s CTCGT 1147s CTCGT 1147s Processing line... 1147s GTAGAACACGAGCCT 1147s GTAGAACACGAGCCT 1147s Processing line... 1147s GTAGAACACGAGCCT 1147s GTAGAACACGAGCCT 1147s Processing line... 1147s GTAGAACACGAGCCT 1147s GTAGAACACGAGCCT 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GGG 1147s GGG 1147s Processing line... 1147s GGG 1147s GGG 1147s Processing line... 1147s GGG 1147s GGG 1147s Processing line... 1147s GGG 1147s GGG 1147s Processing line... 1147s GGG 1147s GGG 1147s Processing line... 1147s GGG 1147s GGG 1147s Processing line... 1147s GGG 1147s GGG 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s ACACGAGCCTGTCACATCGAGATGG 1147s ACACGAGCCTGTCACATCGAGATGG 1147s Processing line... 1147s ACACGAGCCTGTCACATCGAGATGG 1147s ACACGAGCCTGTCACATCGAGATGG 1147s Processing line... 1147s ACACGAGCCTGTCACATCGAGATGG 1147s ACACGAGCCTGTCACATCGAGATGG 1147s Processing line... 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s AT 1147s AT 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GTCACA 1147s GTCACA 1147s Processing line... 1147s GTCACA 1147s GTCACA 1147s Processing line... 1147s GTCACA 1147s GTCACA 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GAGATGGACCACCT 1147s GAGATGGACCACCT 1147s Processing line... 1147s GAGATGGACCACCT 1147s GAGATGGACCACCT 1147s Processing line... 1147s GAGATGGACCACCT 1147s GAGATGGACCACCT 1147s Processing line... 1147s Processing line... 1147s CACGAGCCTG 1147s CACGAGCCTG 1147s Processing line... 1147s CACGAGCCTG 1147s CACGAGCCTG 1147s Processing line... 1147s CACGAGCCTG 1147s CACGAGCCTG 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s CACGAGCC 1147s CACGAGCC 1147s Processing line... 1147s CACGAGCC 1147s CACGAGCC 1147s Processing line... 1147s CACGAGCC 1147s CACGAGCC 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GCCTGTCACAT 1147s GCCTGTCACAT 1147s Processing line... 1147s GCCTGTCACAT 1147s GCCTGTCACAT 1147s Processing line... 1147s GCCTGTCACAT 1147s GCCTGTCACAT 1147s Processing line... 1147s Processing line... 1147s CACATCG 1147s CACATCG 1147s Processing line... 1147s CACATCG 1147s CACATCG 1147s Processing line... 1147s CACATCG 1147s CACATCG 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s CCA 1147s CCA 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s CCA 1147s CCA 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s CCA 1147s CCA 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s CCA 1147s CCA 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s CCA 1147s CCA 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s TGG 1147s TGG 1147s Processing line... 1147s CCA 1147s CCA 1147s Processing line... 1147s CCA 1147s CCA 1147s Processing line... 1147s Processing line... 1147s CTGTCACATCGAGATGG 1147s CTGTCACATCGAGATGG 1147s Processing line... 1147s CTGTCACATCGAGATGG 1147s CTGTCACATCGAGATGG 1147s Processing line... 1147s CTGTCACATCGAGATGG 1147s CTGTCACATCGAGATGG 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GC 1147s GC 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s CGAGATGGA 1147s CGAGATGGA 1147s Processing line... 1147s CGAGATGGA 1147s CGAGATGGA 1147s Processing line... 1147s CGAGATGGA 1147s CGAGATGGA 1147s Processing line... 1147s CAAAACG 1147s CAAAACG 1147s Processing line... 1147s TAGAACACGAGCCTGTC 1147s TAGAACACGAGCCTGTC 1147s Processing line... 1147s TAGAACACGAGCCTGTC 1147s TAGAACACGAGCCTGTC 1147s Processing line... 1147s TAGAACACGAGCCTGTC 1147s TAGAACACGAGCCTGTC 1147s Processing line... 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CC 1147s CC 1147s Processing line... 1147s ATCGAGATGGACCACCTCGTG 1147s ATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s TCACA 1147s TCACA 1147s Processing line... 1147s TCACA 1147s TCACA 1147s Processing line... 1147s TCACA 1147s TCACA 1147s Processing line... 1147s CTCGTGGG 1147s CTCGTGGG 1147s Processing line... 1147s CTCGTGGG 1147s CTCGTGGG 1147s Processing line... 1147s CTCGTGGG 1147s CTCGTGGG 1147s Processing line... 1147s GTC 1147s GTC 1147s Processing line... 1147s GTC 1147s GTC 1147s Processing line... 1147s GAC 1147s GAC 1147s Processing line... 1147s GAC 1147s GAC 1147s Processing line... 1147s GAC 1147s GAC 1147s Processing line... 1147s GAC 1147s GAC 1147s Processing line... 1147s GAC 1147s GAC 1147s Processing line... 1147s GTC 1147s GTC 1147s Processing line... 1147s GAC 1147s GAC 1147s Processing line... 1147s GTC 1147s GTC 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s AACA 1147s AACA 1147s Processing line... 1147s AACA 1147s AACA 1147s Processing line... 1147s AACA 1147s AACA 1147s Processing line... 1147s Processing line... 1147s CCTGTCACATCGAGATGGA 1147s CCTGTCACATCGAGATGGA 1147s Processing line... 1147s CCTGTCACATCGAGATGGA 1147s CCTGTCACATCGAGATGGA 1147s Processing line... 1147s CCTGTCACATCGAGATGGA 1147s CCTGTCACATCGAGATGGA 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s AGGGTCG 1147s AGGGTCG 1147s Processing line... 1147s Processing line... 1147s ACAT 1147s ACAT 1147s Processing line... 1147s ACAT 1147s ACAT 1147s Processing line... 1147s ACAT 1147s ACAT 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s TAGAACACGAGCCTGTCA 1147s TAGAACACGAGCCTGTCA 1147s Processing line... 1147s TAGAACACGAGCCTGTCA 1147s TAGAACACGAGCCTGTCA 1147s Processing line... 1147s TAGAACACGAGCCTGTCA 1147s TAGAACACGAGCCTGTCA 1147s Processing line... 1147s Processing line... 1147s ATAACCAAAACG 1147s ATAACCAAAACG 1147s Processing line... 1147s Processing line... 1147s AGATGGACCACCTCGTG 1147s AGATGGACCACCTCGTG 1147s Processing line... 1147s AGATGGACCACCTCGTG 1147s AGATGGACCACCTCGTG 1147s Processing line... 1147s AGATGGACCACCTCGTG 1147s AGATGGACCACCTCGTG 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GACCACCT 1147s GACCACCT 1147s Processing line... 1147s GACCACCT 1147s GACCACCT 1147s Processing line... 1147s GACCACCT 1147s GACCACCT 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GTAGAAC 1147s GTAGAAC 1147s Processing line... 1147s GTAGAAC 1147s GTAGAAC 1147s Processing line... 1147s GTAGAAC 1147s GTAGAAC 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s CA 1147s CA 1147s Processing line... 1147s TG 1147s TG 1147s Processing line... 1147s Processing line... 1147s AAGT 1147s AAGT 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s TCGTG 1147s TCGTG 1147s Processing line... 1147s TCGTG 1147s TCGTG 1147s Processing line... 1147s CACGA 1147s CACGA 1147s Processing line... 1147s CACGA 1147s CACGA 1147s Processing line... 1147s TCGTG 1147s TCGTG 1147s Processing line... 1147s CACGA 1147s CACGA 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GAGATGGAC 1147s GAGATGGAC 1147s Processing line... 1147s GAGATGGAC 1147s GAGATGGAC 1147s Processing line... 1147s GAGATGGAC 1147s GAGATGGAC 1147s Processing line... 1147s AGAGCTCG 1147s AGAGCTCG 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GAACACGAGCCTGTCACATCGAGATGGACC 1147s GAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GAACACGAGCCTGTCACATCGAGATGGACC 1147s GAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s GAACACGAGCCTGTCACATCGAGATGGACC 1147s GAACACGAGCCTGTCACATCGAGATGGACC 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GCCTGTCACATCGAGATGGACCACC 1147s GCCTGTCACATCGAGATGGACCACC 1147s Processing line... 1147s GCCTGTCACATCGAGATGGACCACC 1147s GCCTGTCACATCGAGATGGACCACC 1147s Processing line... 1147s GCCTGTCACATCGAGATGGACCACC 1147s GCCTGTCACATCGAGATGGACCACC 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s ACATC 1147s ACATC 1147s Processing line... 1147s ACATC 1147s ACATC 1147s Processing line... 1147s ACATC 1147s ACATC 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GACC 1147s GACC 1147s Processing line... 1147s GACC 1147s GACC 1147s Processing line... 1147s GACC 1147s GACC 1147s Processing line... 1147s GGTC 1147s GGTC 1147s Processing line... 1147s GACC 1147s GACC 1147s Processing line... 1147s GTCAC 1147s GTCAC 1147s Processing line... 1147s GTCAC 1147s GTCAC 1147s Processing line... 1147s GTCAC 1147s GTCAC 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GCG 1147s GCG 1147s Processing line... 1147s TGT 1147s TGT 1147s Processing line... 1147s GCG 1147s GCG 1147s Processing line... 1147s TGT 1147s TGT 1147s Processing line... 1147s GCG 1147s GCG 1147s Processing line... 1147s TGT 1147s TGT 1147s Processing line... 1147s GCG 1147s GCG 1147s Processing line... 1147s TGT 1147s TGT 1147s Processing line... 1147s GCG 1147s GCG 1147s Processing line... 1147s TGT 1147s TGT 1147s Processing line... 1147s GCG 1147s GCG 1147s Processing line... 1147s TGT 1147s TGT 1147s Processing line... 1147s TCACATCGAGATGGACCACCTCGTGGG 1147s TCACATCGAGATGGACCACCTCGTGGG 1147s Processing line... 1147s TCACATCGAGATGGACCACCTCGTGGG 1147s TCACATCGAGATGGACCACCTCGTGGG 1147s Processing line... 1147s TCACATCGAGATGGACCACCTCGTGGG 1147s TCACATCGAGATGGACCACCTCGTGGG 1147s Processing line... 1147s Processing line... 1147s TCGA 1147s TCGA 1147s Processing line... 1147s TCGA 1147s TCGA 1147s Processing line... 1147s TCGA 1147s TCGA 1147s Processing line... 1147s TCGA 1147s TCGA 1147s Processing line... 1147s TCGA 1147s TCGA 1147s Processing line... 1147s TCGA 1147s TCGA 1147s Processing line... 1147s TCGA 1147s TCGA 1147s Processing line... 1147s TCGA 1147s TCGA 1147s Processing line... 1147s TCGA 1147s TCGA 1147s Processing line... 1147s TCGA 1147s TCGA 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s CACATCGAGATGGACCA 1147s CACATCGAGATGGACCA 1147s Processing line... 1147s CACATCGAGATGGACCA 1147s CACATCGAGATGGACCA 1147s Processing line... 1147s CACATCGAGATGGACCA 1147s CACATCGAGATGGACCA 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s ACACGAGCCTGTCACATCGAG 1147s ACACGAGCCTGTCACATCGAG 1147s Processing line... 1147s ACACGAGCCTGTCACATCGAG 1147s ACACGAGCCTGTCACATCGAG 1147s Processing line... 1147s ACACGAGCCTGTCACATCGAG 1147s ACACGAGCCTGTCACATCGAG 1147s Processing line... 1147s Processing line... 1147s AACC 1147s AACC 1147s Processing line... 1147s AACC 1147s AACC 1147s Processing line... 1147s AACC 1147s AACC 1147s Processing line... 1147s AACC 1147s AACC 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s TAGAACA 1147s TAGAACA 1147s Processing line... 1147s TAGAACA 1147s TAGAACA 1147s Processing line... 1147s TAGAACA 1147s TAGAACA 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s CTCG 1147s CTCG 1147s Processing line... 1147s CTCG 1147s CTCG 1147s Processing line... 1147s CGAG 1147s CGAG 1147s Processing line... 1147s CTCG 1147s CTCG 1147s Processing line... 1147s CGAG 1147s CGAG 1147s Processing line... 1147s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 4 --large-index --score-min L,5.57610935390429,7.38388055778567 -a -r -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1147s CGAG 1147s CGAG 1147s Processing line... 1147s CGAG 1147s CGAG 1147s Processing line... 1147s CGAG 1147s CGAG 1147s Processing line... 1147s CTCG 1147s CTCG 1147s Processing line... 1147s CGAG 1147s CGAG 1147s Processing line... 1147s CGAG 1147s CGAG 1147s Processing line... 1147s Processing line... 1147s TGGATAACCAAAAC 1147s TGGATAACCAAAAC 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s AGTAGAACACGAGCCTGT 1147s AGTAGAACACGAGCCTGT 1147s Processing line... 1147s AGTAGAACACGAGCCTGT 1147s AGTAGAACACGAGCCTGT 1147s Processing line... 1147s AGTAGAACACGAGCCTGT 1147s AGTAGAACACGAGCCTGT 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s CTGTCACATCGAGATGGACCACCTCGTG 1147s CTGTCACATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CTGTCACATCGAGATGGACCACCTCGTG 1147s CTGTCACATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s CTGTCACATCGAGATGGACCACCTCGTG 1147s CTGTCACATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s ATCGAGATGGACCA 1147s ATCGAGATGGACCA 1147s Processing line... 1147s ATCGAGATGGACCA 1147s ATCGAGATGGACCA 1147s Processing line... 1147s ATCGAGATGGACCA 1147s ATCGAGATGGACCA 1147s Processing line... 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1147s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1147s Processing line... 1147s Processing line... 1147s TAACCA 1147s TAACCA 1147s Processing line... 1147s TAACCA 1147s TAACCA 1147s Processing line... 1147s TAACCA 1147s TAACCA 1147s Processing line... 1147s TAACCA 1147s TAACCA 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s CGAGCCTGTCACATCGAGAT 1147s CGAGCCTGTCACATCGAGAT 1147s Processing line... 1147s CGAGCCTGTCACATCGAGAT 1147s CGAGCCTGTCACATCGAGAT 1147s Processing line... 1147s CGAGCCTGTCACATCGAGAT 1147s CGAGCCTGTCACATCGAGAT 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s TC 1147s TC 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s GA 1147s GA 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s ACACGAGCCTGTCACAT 1147s ACACGAGCCTGTCACAT 1147s Processing line... 1147s ACACGAGCCTGTCACAT 1147s ACACGAGCCTGTCACAT 1147s Processing line... 1147s ACACGAGCCTGTCACAT 1147s ACACGAGCCTGTCACAT 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s ACACGAGCCTGT 1147s ACACGAGCCTGT 1147s Processing line... 1147s ACACGAGCCTGT 1147s ACACGAGCCTGT 1147s Processing line... 1147s ACACGAGCCTGT 1147s ACACGAGCCTGT 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s TGGACCA 1147s TGGACCA 1147s Processing line... 1147s TGGACCA 1147s TGGACCA 1147s Processing line... 1147s TGGACCA 1147s TGGACCA 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s Processing line... 1147s --- Summary --- 1147s Read 1 reference strings 1147s Checked 395 alignments, 0 edits 1147s --------------- 1147s PASSED 1147s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1147s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 1147s Warning: skipping mate #2 of read '5' because it was < 2 characters long 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1147s Warning: skipping mate #1 of read '50' because length (1) <= # seed mismatches (0) 1147s Warning: skipping mate #1 of read '50' because it was < 2 characters long 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1147s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 1147s Warning: skipping mate #2 of read '56' because it was < 2 characters long 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1147s Warning: skipping mate #1 of read '97' because length (1) <= # seed mismatches (0) 1147s Warning: skipping mate #1 of read '97' because it was < 2 characters long 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 1147s Warning: skipping mate #1 of read '137' because length (1) <= # seed mismatches (0) 1147s Warning: skipping mate #1 of read '137' because it was < 2 characters long 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 1147s Warning: skipping mate #2 of read '141' because length (1) <= # seed mismatches (0) 1147s Warning: skipping mate #2 of read '141' because it was < 2 characters long 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 1147s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 1147s 171 reads; of these: 1147s 171 (100.00%) were paired; of these: 1147s 167 (97.66%) aligned concordantly 0 times 1147s 0 (0.00%) aligned concordantly exactly 1 time 1147s 4 (2.34%) aligned concordantly >1 times 1147s ---- 1147s 167 pairs aligned concordantly 0 times; of these: 1147s 0 (0.00%) aligned discordantly 1 time 1147s ---- 1147s 167 pairs aligned 0 times concordantly or discordantly; of these: 1147s 334 mates make up the pairs; of these: 1147s 276 (82.63%) aligned 0 times 1147s 6 (1.80%) aligned exactly 1 time 1147s 52 (15.57%) aligned >1 times 1147s 19.30% overall alignment rate 1147s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1147s Flattened IUPAC characters 1147s Mutating sequence Sim.pm.1 1147s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1147s Finished SNPs 1147s Finished ref gaps 1147s Finished read gaps 1147s Mutating sequence Sim.pm.2 1147s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1147s Finished SNPs 1147s Finished ref gaps 1147s Finished read gaps 1147s Mutated reference genome to subject genome 1147s SNPs introduced: 6 1147s Reference gaps introduced: 0 1147s Read gaps introduced: 0 1147s Rearrangements introduced: 0 1147s Created read sampler 1147s Sampling 85 reads 1147s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1147s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1147s *** Run 48 of 100 1147s /usr/bin/bowtie2 --cp-ival 2 --cp-min 3 --large-index --ma 26.6440446356981 -k 3 --trim3 8 --np 4 --norc --score-min L,7.87810898276012,3.83268309793345 --trim5 0 -i S,0.993723484904736 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1147s parsing sequence Sim.pm.1... 1147s parsing sequence Sim.pm.2... 1147s Parsed 269 reference bases 1147s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1148s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '1' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1148s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '2' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1148s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1148s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '10' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1148s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1148s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1148s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1148s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1148s Warning: skipping read '37' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1148s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1148s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1148s Read 50 alignments... 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1148s Read 100 alignments... 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1148s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1148s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1148s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1148s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '62' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1148s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '64' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1148s Warning: skipping mate #1 of read '73' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1148s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '76' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1148s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '79' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1148s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '80' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1148s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '81' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1148s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 1148s Warning: skipping read '83' because it was < 2 characters long 1148s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1148s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1148s 85 reads; of these: 1148s 73 (85.88%) were paired; of these: 1148s 71 (97.26%) aligned concordantly 0 times 1148s 0 (0.00%) aligned concordantly exactly 1 time 1148s 2 (2.74%) aligned concordantly >1 times 1148s ---- 1148s 71 pairs aligned concordantly 0 times; of these: 1148s 0 (0.00%) aligned discordantly 1 time 1148s ---- 1148s 71 pairs aligned 0 times concordantly or discordantly; of these: 1148s 142 mates make up the pairs; of these: 1148s 121 (85.21%) aligned 0 times 1148s 4 (2.82%) aligned exactly 1 time 1148s 17 (11.97%) aligned >1 times 1148s 12 (14.12%) were unpaired; of these: 1148s 9 (75.00%) aligned 0 times 1148s 0 (0.00%) aligned exactly 1 time 1148s 3 (25.00%) aligned >1 times 1148s 17.72% overall alignment rate 1148s Read 150 alignments... 1148s Read 200 alignments... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s CA 1148s CA 1148s Processing line... 1148s CA 1148s CA 1148s Processing line... 1148s CA 1148s CA 1148s Processing line... 1148s Processing line... 1148s CATCGAGATGGACCA 1148s CATCGAGATGGACCA 1148s Processing line... 1148s CATCGAGATGGACCA 1148s CATCGAGATGGACCA 1148s Processing line... 1148s CATCGAGATGGACCA 1148s CATCGAGATGGACCA 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s GA 1148s GA 1148s Processing line... 1148s GA 1148s GA 1148s Processing line... 1148s GA 1148s GA 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s CCTGTCACATCGAGATGGACCACCT 1148s CCTGTCACATCGAGATGGACCACCT 1148s Processing line... 1148s CCTGTCACATCGAGATGGACCACCT 1148s CCTGTCACATCGAGATGGACCACCT 1148s Processing line... 1148s CCTGTCACATCGAGATGGACCACCT 1148s CCTGTCACATCGAGATGGACCACCT 1148s Processing line... 1148s Processing line... 1148s ACG 1148s ACG 1148s Processing line... 1148s ACG 1148s ACG 1148s Processing line... 1148s ACG 1148s ACG 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s CG 1148s CG 1148s Processing line... 1148s CG 1148s CG 1148s Processing line... 1148s CG 1148s CG 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1148s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1148s Processing line... 1148s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1148s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1148s Processing line... 1148s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1148s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1148s Processing line... 1148s Processing line... 1148s AG 1148s AG 1148s Processing line... 1148s AG 1148s AG 1148s Processing line... 1148s AG 1148s AG 1148s Processing line... 1148s Processing line... 1148s AT 1148s AT 1148s Processing line... 1148s AT 1148s AT 1148s Processing line... 1148s AT 1148s AT 1148s Processing line... 1148s Processing line... 1148s GTGAGGGT 1148s GTGAGGGT 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s CACGAGCCTGTC 1148s CACGAGCCTGTC 1148s Processing line... 1148s CACGAGCCTGTC 1148s CACGAGCCTGTC 1148s Processing line... 1148s CACGAGCCTGTC 1148s CACGAGCCTGTC 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s CGT 1148s CGT 1148s Processing line... 1148s CGT 1148s CGT 1148s Processing line... 1148s CGT 1148s CGT 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s ACCAC 1148s ACCAC 1148s Processing line... 1148s AACACGAGCCTGTCACATC 1148s AACACGAGCCTGTCACATC 1148s Processing line... 1148s ACCAC 1148s ACCAC 1148s Processing line... 1148s AACACGAGCCTGTCACATC 1148s AACACGAGCCTGTCACATC 1148s Processing line... 1148s ACCAC 1148s ACCAC 1148s Processing line... 1148s AACACGAGCCTGTCACATC 1148s AACACGAGCCTGTCACATC 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s CA 1148s CA 1148s Processing line... 1148s CA 1148s CA 1148s Processing line... 1148s CA 1148s CA 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s GAGCCTG 1148s GAGCCTG 1148s Processing line... 1148s GAGCCTG 1148s GAGCCTG 1148s Processing line... 1148s GAGCCTG 1148s GAGCCTG 1148s Processing line... 1148s Processing line... 1148s ATC 1148s ATC 1148s Processing line... 1148s ATC 1148s ATC 1148s Processing line... 1148s ATC 1148s ATC 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s GA 1148s GA 1148s Processing line... 1148s GA 1148s GA 1148s Processing line... 1148s GA 1148s GA 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s GCTCGCA 1148s GCTCGCA 1148s Processing line... 1148s Processing line... 1148s CGAGCCTGTCACATCGAGATGGACCACCTCGT 1148s CGAGCCTGTCACATCGAGATGGACCACCTCGT 1148s Processing line... 1148s CGAGCCTGTCACATCGAGATGGACCACCTCGT 1148s CGAGCCTGTCACATCGAGATGGACCACCTCGT 1148s Processing line... 1148s CGAGCCTGTCACATCGAGATGGACCACCTCGT 1148s CGAGCCTGTCACATCGAGATGGACCACCTCGT 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s ATAACCAAAAC 1148s ATAACCAAAAC 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s CGAGATGGACCACCTCGTG 1148s CGAGATGGACCACCTCGTG 1148s Processing line... 1148s CGAGATGGACCACCTCGTG 1148s CGAGATGGACCACCTCGTG 1148s Processing line... 1148s CGAGATGGACCACCTCGTG 1148s CGAGATGGACCACCTCGTG 1148s Processing line... 1148s Processing line... 1148s GCCT 1148s GCCT 1148s Processing line... 1148s GCCT 1148s GCCT 1148s Processing line... 1148s GCCT 1148s GCCT 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s AGCC 1148s AGCC 1148s Processing line... 1148s AGCC 1148s AGCC 1148s Processing line... 1148s AGCC 1148s AGCC 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s GG 1148s GG 1148s Processing line... 1148s GAGATGGACCACCTCG 1148s GAGATGGACCACCTCG 1148s Processing line... 1148s GG 1148s GG 1148s Processing line... 1148s GAGATGGACCACCTCG 1148s GAGATGGACCACCTCG 1148s Processing line... 1148s GG 1148s GG 1148s Processing line... 1148s GAGATGGACCACCTCG 1148s GAGATGGACCACCTCG 1148s Processing line... 1148s TG 1148s TG 1148s Processing line... 1148s TG 1148s TG 1148s Processing line... 1148s TG 1148s TG 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s GCA 1148s GCA 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s --- Summary --- 1148s Read 1 reference strings 1148s Checked 76 alignments, 0 edits 1148s --------------- 1148s PASSED 1148s Flattened IUPAC characters 1148s Mutating sequence Sim.pm.2 1148s Introducing 11 SNPs, 3/1 ref/read gaps, and 0 rearrangements 1148s Finished SNPs 1148s Finished ref gaps 1148s Finished read gaps 1148s Mutating sequence Sim.pm.1 1148s Introducing 2 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1148s Finished SNPs 1148s Finished ref gaps 1148s Finished read gaps 1148s Mutated reference genome to subject genome 1148s SNPs introduced: 13 1148s Reference gaps introduced: 4 1148s Read gaps introduced: 2 1148s Rearrangements introduced: 0 1148s Created read sampler 1148s Sampling 64 reads 1148s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1148s *** Run 49 of 100 1148s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 10 -k 11 --large-index --local -D 15 --norc --nofw --np 2 --score-min L,7.14999362814681,2.02615199667538 --rfg 9.1455803925052,15.487822584093 --trim5 5 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1148s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1148s parsing sequence Sim.pm.1... 1148s parsing sequence Sim.pm.2... 1148s Parsed 269 reference bases 1148s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1148s Warning: skipping read '2' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '40' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '50' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1148s 64 reads; of these: 1148s 58 (90.62%) were paired; of these: 1148s 58 (100.00%) aligned concordantly 0 times 1148s 0 (0.00%) aligned concordantly exactly 1 time 1148s 0 (0.00%) aligned concordantly >1 times 1148s ---- 1148s 58 pairs aligned concordantly 0 times; of these: 1148s 0 (0.00%) aligned discordantly 1 time 1148s ---- 1148s 58 pairs aligned 0 times concordantly or discordantly; of these: 1148s 116 mates make up the pairs; of these: 1148s 116 (100.00%) aligned 0 times 1148s 0 (0.00%) aligned exactly 1 time 1148s 0 (0.00%) aligned >1 times 1148s 6 (9.38%) were unpaired; of these: 1148s 6 (100.00%) aligned 0 times 1148s 0 (0.00%) aligned exactly 1 time 1148s 0 (0.00%) aligned >1 times 1148s 0.00% overall alignment rate 1148s Read 50 alignments... 1148s Read 100 alignments... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 10 -k 11 --large-index --local -D 15 --norc --nofw --np 2 --score-min L,7.14999362814681,2.02615199667538 --rfg 9.1455803925052,15.487822584093 --trim5 5 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s Processing line... 1148s --- Summary --- 1148s Read 1 reference strings 1148s Checked 0 alignments, 0 edits 1148s --------------- 1148s PASSED 1148s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1148s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1148s Warning: skipping read '2' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '40' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '50' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1148s 64 reads; of these: 1148s 58 (90.62%) were paired; of these: 1148s 58 (100.00%) aligned concordantly 0 times 1148s 0 (0.00%) aligned concordantly exactly 1 time 1148s 0 (0.00%) aligned concordantly >1 times 1148s ---- 1148s 58 pairs aligned concordantly 0 times; of these: 1148s 0 (0.00%) aligned discordantly 1 time 1148s ---- 1148s 58 pairs aligned 0 times concordantly or discordantly; of these: 1148s 116 mates make up the pairs; of these: 1148s 116 (100.00%) aligned 0 times 1148s 0 (0.00%) aligned exactly 1 time 1148s 0 (0.00%) aligned >1 times 1148s 6 (9.38%) were unpaired; of these: 1148s 6 (100.00%) aligned 0 times 1148s 0 (0.00%) aligned exactly 1 time 1148s 0 (0.00%) aligned >1 times 1148s 0.00% overall alignment rate 1148s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1148s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1148s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1148s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1148s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 10 -k 11 --large-index --local -D 15 --norc --nofw --np 2 --score-min L,7.14999362814681,2.02615199667538 --rfg 9.1455803925052,15.487822584093 --trim5 5 -q -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1148s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1148s Warning: skipping read '2' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '6' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '14' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '19' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '40' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1148s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 1148s Warning: skipping mate #2 of read '50' because it was < 2 characters long 1148s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1148s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1148s 64 reads; of these: 1148s 58 (90.62%) were paired; of these: 1148s 58 (100.00%) aligned concordantly 0 times 1148s 0 (0.00%) aligned concordantly exactly 1 time 1148s 0 (0.00%) aligned concordantly >1 times 1148s ---- 1148s 58 pairs aligned concordantly 0 times; of these: 1148s 0 (0.00%) aligned discordantly 1 time 1148s ---- 1148s 58 pairs aligned 0 times concordantly or discordantly; of these: 1148s 116 mates make up the pairs; of these: 1148s 116 (100.00%) aligned 0 times 1148s 0 (0.00%) aligned exactly 1 time 1148s 0 (0.00%) aligned >1 times 1148s 6 (9.38%) were unpaired; of these: 1148s 6 (100.00%) aligned 0 times 1148s 0 (0.00%) aligned exactly 1 time 1148s 0 (0.00%) aligned >1 times 1148s 0.00% overall alignment rate 1148s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1148s Flattened IUPAC characters 1148s Mutating sequence Sim.pm.2 1148s Introducing 13 SNPs, 0/1 ref/read gaps, and 3 rearrangements 1148s Finished SNPs 1148s Finished ref gaps 1148s Finished read gaps 1148s Mutating sequence Sim.pm.1 1148s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1148s Finished SNPs 1148s Finished ref gaps 1148s Finished read gaps 1148s Mutated reference genome to subject genome 1148s SNPs introduced: 16 1148s Reference gaps introduced: 0 1148s Read gaps introduced: 1 1148s Rearrangements introduced: 4 1148s Created read sampler 1148s Sampling 69 reads 1148s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1148s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1148s parsing sequence Sim.pm.1... 1148s parsing sequence Sim.pm.2... 1148s Parsed 269 reference bases 1148s *** Run 50 of 100 1148s /usr/bin/bowtie2 --score-min L,1.39917457566123,3.98168367028381 --rfg 1.47910070499571,2.11174762179076 -R 4 --np 2 --large-index -k 7 --rdg 17.7650587340025 --cp-ival 1 --mm --cp-min 5 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1149s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 1149s Warning: skipping read '36' because it was < 2 characters long 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1149s 69 reads; of these: 1149s 69 (100.00%) were unpaired; of these: 1149s 55 (79.71%) aligned 0 times 1149s 4 (5.80%) aligned exactly 1 time 1149s 10 (14.49%) aligned >1 times 1149s 20.29% overall alignment rate 1149s Read 50 alignments... 1149s Read 100 alignments... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s CAAA 1149s CAAA 1149s Processing line... 1149s GAAATTAGAGCTCGCAGCGCG 1149s GAAATTAGAGCTCGCAGCGCG 1149s Processing line... 1149s TCGT 1149s TCGT 1149s Processing line... 1149s TCGT 1149s TCGT 1149s Processing line... 1149s TCGT 1149s TCGT 1149s Processing line... 1149s ACGA 1149s ACGA 1149s Processing line... 1149s ACGA 1149s ACGA 1149s Processing line... 1149s ACGA 1149s ACGA 1149s Processing line... 1149s GAGATGG 1149s GAGATGG 1149s Processing line... 1149s GAGATGG 1149s GAGATGG 1149s Processing line... 1149s GAGATGG 1149s GAGATGG 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s GCTCGCA 1149s GCTCGCA 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s CACGAGCCTGTCACAT 1149s CACGAGCCTGTCACAT 1149s Processing line... 1149s CACGAGCCTGTCACAT 1149s CACGAGCCTGTCACAT 1149s Processing line... 1149s CACGAGCCTGTCACAT 1149s CACGAGCCTGTCACAT 1149s Processing line... 1149s CCACC 1149s CCACC 1149s Processing line... 1149s CCACC 1149s CCACC 1149s Processing line... 1149s CCACC 1149s CCACC 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s CGAG 1149s CGAG 1149s Processing line... 1149s CGAG 1149s CGAG 1149s Processing line... 1149s CGAG 1149s CGAG 1149s Processing line... 1149s CGAG 1149s CGAG 1149s Processing line... 1149s CGAG 1149s CGAG 1149s Processing line... 1149s CGAG 1149s CGAG 1149s Processing line... 1149s CGAG 1149s CGAG 1149s Processing line... 1149s Processing line... 1149s AACACGAGCCTGTCACATCGAGATGGACCACCTCGT 1149s AACACGAGCCTGTCACATCGAGATGGACCACCTCGT 1149s Processing line... 1149s AACACGAGCCTGTCACATCGAGATGGACCACCTCGT 1149s AACACGAGCCTGTCACATCGAGATGGACCACCTCGT 1149s Processing line... 1149s AACACGAGCCTGTCACATCGAGATGGACCACCTCGT 1149s AACACGAGCCTGTCACATCGAGATGGACCACCTCGT 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s AGA 1149s AGA 1149s Processing line... 1149s AGA 1149s AGA 1149s Processing line... 1149s AGA 1149s AGA 1149s Processing line... 1149s AGA 1149s AGA 1149s Processing line... 1149s AGA 1149s AGA 1149s Processing line... 1149s AGA 1149s AGA 1149s Processing line... 1149s AGA 1149s AGA 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s ATGGACCACCT 1149s ATGGACCACCT 1149s Processing line... 1149s ATGGACCACCT 1149s ATGGACCACCT 1149s Processing line... 1149s ATGGACCACCT 1149s ATGGACCACCT 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s ATGGTGAGGGTCG 1149s ATGGTGAGGGTCG 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s AGTAGAACACGAGCCTGTCACATCGAGATGGACCA 1149s AGTAGAACACGAGCCTGTCACATCGAGATGGACCA 1149s Processing line... 1149s AGTAGAACACGAGCCTGTCACATCGAGATGGACCA 1149s AGTAGAACACGAGCCTGTCACATCGAGATGGACCA 1149s Processing line... 1149s AGTAGAACACGAGCCTGTCACATCGAGATGGACCA 1149s AGTAGAACACGAGCCTGTCACATCGAGATGGACCA 1149s Processing line... 1149s Processing line... 1149s TGG 1149s TGG 1149s Processing line... 1149s TGG 1149s TGG 1149s Processing line... 1149s TGG 1149s TGG 1149s Processing line... 1149s TGG 1149s TGG 1149s Processing line... 1149s TGG 1149s TGG 1149s Processing line... 1149s TGG 1149s TGG 1149s Processing line... 1149s TGG 1149s TGG 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s Processing line... 1149s --- Summary --- 1149s Read 1 reference strings 1149s Checked 49 alignments, 0 edits 1149s --------------- 1149s PASSED 1149s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1149s /usr/bin/bowtie2 --score-min L,1.39917457566123,3.98168367028381 --rfg 1.47910070499571,2.11174762179076 -R 4 --np 2 --large-index -k 7 --rdg 17.7650587340025 --cp-ival 1 --mm --cp-min 5 -f -p 2 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1149s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 1149s Warning: skipping read '36' because it was < 2 characters long 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1149s 69 reads; of these: 1149s 69 (100.00%) were unpaired; of these: 1149s 55 (79.71%) aligned 0 times 1149s 4 (5.80%) aligned exactly 1 time 1149s 10 (14.49%) aligned >1 times 1149s 20.29% overall alignment rate 1149s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1149s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1149s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1149s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1149s /usr/bin/bowtie2 --score-min L,1.39917457566123,3.98168367028381 --rfg 1.47910070499571,2.11174762179076 -R 4 --np 2 --large-index -k 7 --rdg 17.7650587340025 --cp-ival 1 --mm --cp-min 5 -f -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1149s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 1149s Warning: skipping read '36' because it was < 2 characters long 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1149s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1149s 69 reads; of these: 1149s 69 (100.00%) were unpaired; of these: 1149s 55 (79.71%) aligned 0 times 1149s 4 (5.80%) aligned exactly 1 time 1149s 10 (14.49%) aligned >1 times 1149s 20.29% overall alignment rate 1149s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1149s Flattened IUPAC characters 1149s Mutating sequence Sim.pm.1 1149s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1149s Finished SNPs 1149s Finished ref gaps 1149s Finished read gaps 1149s Mutating sequence Sim.pm.2 1149s Introducing 15 SNPs, 0/3 ref/read gaps, and 1 rearrangements 1149s Finished SNPs 1149s Finished ref gaps 1149s Finished read gaps 1149s Mutated reference genome to subject genome 1149s SNPs introduced: 18 1149s Reference gaps introduced: 0 1149s Read gaps introduced: 3 1149s Rearrangements introduced: 2 1149s Created read sampler 1149s Sampling 126 reads 1149s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1149s *** Run 51 of 100 1149s /usr/bin/bowtie2 --trim3 2 --local -M 12 --large-index --cp-min 2 --cp-ival 1 --trim5 5 --n-ceil 1.40024677082942,0.220606401446995 --score-min L,6.63408086676936,1.51322894712186 --np 6 -R 3 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1149s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1149s parsing sequence Sim.pm.1... 1149s parsing sequence Sim.pm.2... 1149s Parsed 269 reference bases 1149s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1149s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 1149s Warning: skipping read '0' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1150s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1150s Warning: skipping read '28' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1150s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 1150s Warning: skipping read '40' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '57' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '69' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '72' because it was < 2 characters long 1150s Read 50 alignments... 1150s Read 100 alignments... 1150s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '76' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '79' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '80' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '82' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '87' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '88' because it was < 2 characters long 1150s Warning: skipping mate #2 of read '88' because it was < 2 characters long 1150s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 1150s Warning: skipping read '100' because it was < 2 characters long 1150s Warning: skipping mate #2 of read '111' because length (1) <= # seed mismatches (0) 1150s Warning: skipping mate #2 of read '111' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '119' because it was < 2 characters long 1150s Warning: skipping mate #2 of read '122' because length (1) <= # seed mismatches (0) 1150s Warning: skipping mate #2 of read '122' because it was < 2 characters long 1150s 126 reads; of these: 1150s 103 (81.75%) were paired; of these: 1150s 102 (99.03%) aligned concordantly 0 times 1150s 0 (0.00%) aligned concordantly exactly 1 time 1150s 1 (0.97%) aligned concordantly >1 times 1150s ---- 1150s 102 pairs aligned concordantly 0 times; of these: 1150s 1 (0.98%) aligned discordantly 1 time 1150s ---- 1150s 101 pairs aligned 0 times concordantly or discordantly; of these: 1150s 202 mates make up the pairs; of these: 1150s 184 (91.09%) aligned 0 times 1150s 6 (2.97%) aligned exactly 1 time 1150s 12 (5.94%) aligned >1 times 1150s 23 (18.25%) were unpaired; of these: 1150s 22 (95.65%) aligned 0 times 1150s 1 (4.35%) aligned exactly 1 time 1150s 0 (0.00%) aligned >1 times 1150s 10.04% overall alignment rate 1150s Read 150 alignments... 1150s Read 200 alignments... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s AGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGATAACCA 1150s AGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCA 1150s Processing line... 1150s Processing line... 1150s CACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGATAACCAGAGTAGAACACGAGCCTGTC 1150s CACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTC 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s AGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGAGAAC 1150s AGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAAC 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s GTCACATCGAGATGGACCACCTCGTAGGTTGGATAACCATAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1150s GTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s CGGCTGAAGTGGCTG 1150s CGGCTGAAGTGGCTG 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s AACACGAGCCTGTCACATCGAGATGGAC 1150s AACACGAGCCTGTCACATCGAGATGGAC 1150s Processing line... 1150s TGGGATGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCA 1150s TGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCA 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s ACATCGAGATGGACCACCTCGTG 1150s ACATCGAGATGGACCACCTCGTG 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACC 1150s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACC 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s GAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAG-CTGTCACATCGAGATGGACCACCTCGTAGGTTGGATAACCATAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGAGAACCAAAAC 1150s GAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAAC 1150s Processing line... 1150s Processing line... 1150s AGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACG 1150s AGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACG 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s AGTAGAACACGAGCCTGTCACATCGAG 1150s AGTAGAACACGAGCCTGTCACATCGAG 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s CGAGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAG-CTGTCACATCGAGATGGACCACCTCGTAGG 1150s CGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGT-GG 1150s Processing line... 1150s ACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAG-CTGTCACATCGAGATGGACCACCTC--G 1150s ACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s GGGGTATGGTGAGG 1150s GGGGTATGGTGAGG 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s CACGAGCCTGTCACATCG 1150s CACGAGCCTGTCACATCG 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s TAACCATAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGAGAACCAAAACG 1150s TAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAACG 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s CGAGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGATAACCA 1150s CGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCA 1150s Processing line... 1150s Processing line... 1150s TAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTTGGAGAACCAAAACGCGGAAATTA 1150s TAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAAACGCNGAAATTA 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s ACATCGAGATGGACCACCTCGT 1150s ACATCGAGATGGACCACCTCGT 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s CCACCTCGTGGGATGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAG-CTGTCACATCGAGATGGACCACCTCGTAGGTTGGAT 1150s CCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGAT 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s ATAACCATAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGTT 1150s ATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNT 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s GGGGTATGGTGAGGGTCGAGGACC 1150s GGGGTATGGTGAGGGTCGAGGACC 1150s Processing line... 1150s --- Summary --- 1150s Read 1 reference strings 1150s Checked 23 alignments, 0 edits 1150s --------------- 1150s PASSED 1150s Flattened IUPAC characters 1150s Mutating sequence Sim.pm.1 1150s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1150s Finished SNPs 1150s Finished ref gaps 1150s Finished read gaps 1150s Mutating sequence Sim.pm.2 1150s Introducing 21 SNPs, 0/1 ref/read gaps, and 3 rearrangements 1150s Finished SNPs 1150s Finished ref gaps 1150s Finished read gaps 1150s Mutated reference genome to subject genome 1150s SNPs introduced: 21 1150s Reference gaps introduced: 1 1150s Read gaps introduced: 2 1150s Rearrangements introduced: 3 1150s Created read sampler 1150s Sampling 52 reads 1150s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1150s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1150s parsing sequence Sim.pm.1... 1150s parsing sequence Sim.pm.2... 1150s Parsed 269 reference bases 1150s *** Run 52 of 100 1150s /usr/bin/bowtie2 --score-min L,1.12708502113923,9.16874425408582 --rfg 44.1166559168677 --trim5 1 -R 4 --np 1 --large-index --local --trim3 7 --cp-ival 1 --cp-min 2 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1150s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1150s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1150s Warning: skipping read '32' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '50' because it was < 2 characters long 1150s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1150s Warning: skipping read '52' because it was < 2 characters long 1150s 52 reads; of these: 1150s 46 (88.46%) were paired; of these: 1150s 46 (100.00%) aligned concordantly 0 times 1150s 0 (0.00%) aligned concordantly exactly 1 time 1150s 0 (0.00%) aligned concordantly >1 times 1150s ---- 1150s 46 pairs aligned concordantly 0 times; of these: 1150s 0 (0.00%) aligned discordantly 1 time 1150s ---- 1150s 46 pairs aligned 0 times concordantly or discordantly; of these: 1150s 92 mates make up the pairs; of these: 1150s 92 (100.00%) aligned 0 times 1150s 0 (0.00%) aligned exactly 1 time 1150s 0 (0.00%) aligned >1 times 1150s 6 (11.54%) were unpaired; of these: 1150s 6 (100.00%) aligned 0 times 1150s 0 (0.00%) aligned exactly 1 time 1150s 0 (0.00%) aligned >1 times 1150s 0.00% overall alignment rate 1150s Read 50 alignments... 1150s Read 100 alignments... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s /usr/bin/bowtie2 --score-min L,1.12708502113923,9.16874425408582 --rfg 44.1166559168677 --trim5 1 -R 4 --np 1 --large-index --local --trim3 7 --cp-ival 1 --cp-min 2 -f -p 3 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s Processing line... 1150s --- Summary --- 1150s Read 1 reference strings 1150s Checked 0 alignments, 0 edits 1150s --------------- 1150s PASSED 1150s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1150s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '50' because it was < 2 characters long 1150s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1150s Warning: skipping read '52' because it was < 2 characters long 1150s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1150s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1150s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1150s Warning: skipping read '32' because it was < 2 characters long 1150s 52 reads; of these: 1150s 46 (88.46%) were paired; of these: 1150s 46 (100.00%) aligned concordantly 0 times 1150s 0 (0.00%) aligned concordantly exactly 1 time 1150s 0 (0.00%) aligned concordantly >1 times 1150s ---- 1150s 46 pairs aligned concordantly 0 times; of these: 1150s 0 (0.00%) aligned discordantly 1 time 1150s ---- 1150s 46 pairs aligned 0 times concordantly or discordantly; of these: 1150s 92 mates make up the pairs; of these: 1150s 92 (100.00%) aligned 0 times 1150s 0 (0.00%) aligned exactly 1 time 1150s 0 (0.00%) aligned >1 times 1150s 6 (11.54%) were unpaired; of these: 1150s 6 (100.00%) aligned 0 times 1150s 0 (0.00%) aligned exactly 1 time 1150s 0 (0.00%) aligned >1 times 1150s 0.00% overall alignment rate 1150s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1150s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1150s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1150s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1150s /usr/bin/bowtie2 --score-min L,1.12708502113923,9.16874425408582 --rfg 44.1166559168677 --trim5 1 -R 4 --np 1 --large-index --local --trim3 7 --cp-ival 1 --cp-min 2 -f -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1151s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1151s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1151s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1151s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '17' because it was < 2 characters long 1151s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '19' because it was < 2 characters long 1151s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1151s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '32' because it was < 2 characters long 1151s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1151s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '50' because it was < 2 characters long 1151s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1151s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1151s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 1151s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1151s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '52' because it was < 2 characters long 1151s 52 reads; of these: 1151s 46 (88.46%) were paired; of these: 1151s 46 (100.00%) aligned concordantly 0 times 1151s 0 (0.00%) aligned concordantly exactly 1 time 1151s 0 (0.00%) aligned concordantly >1 times 1151s ---- 1151s 46 pairs aligned concordantly 0 times; of these: 1151s 0 (0.00%) aligned discordantly 1 time 1151s ---- 1151s 46 pairs aligned 0 times concordantly or discordantly; of these: 1151s 92 mates make up the pairs; of these: 1151s 92 (100.00%) aligned 0 times 1151s 0 (0.00%) aligned exactly 1 time 1151s 0 (0.00%) aligned >1 times 1151s 6 (11.54%) were unpaired; of these: 1151s 6 (100.00%) aligned 0 times 1151s 0 (0.00%) aligned exactly 1 time 1151s 0 (0.00%) aligned >1 times 1151s 0.00% overall alignment rate 1151s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1151s Flattened IUPAC characters 1151s Mutating sequence Sim.pm.2 1151s Introducing 21 SNPs, 0/2 ref/read gaps, and 1 rearrangements 1151s Finished SNPs 1151s Finished ref gaps 1151s Finished read gaps 1151s Mutating sequence Sim.pm.1 1151s Introducing 13 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1151s Finished SNPs 1151s Finished ref gaps 1151s Finished read gaps 1151s Mutated reference genome to subject genome 1151s SNPs introduced: 34 1151s Reference gaps introduced: 1 1151s Read gaps introduced: 2 1151s Rearrangements introduced: 1 1151s Created read sampler 1151s Sampling 140 reads 1151s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1151s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1151s parsing sequence Sim.pm.1... 1151s parsing sequence Sim.pm.2... 1151s Parsed 269 reference bases 1151s *** Run 53 of 100 1151s /usr/bin/bowtie2 --cp-ival 4 --cp-min 2 --large-index --trim3 9 --rdg 34.333699960897,16.2113109975874 --local -R 1 --nofw --norc --score-min L,4.50683359107042,9.26799630549722 -i L,0.17458957333123 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1151s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '2' because it was < 2 characters long 1151s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '4' because it was < 2 characters long 1151s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '5' because it was < 2 characters long 1151s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '6' because it was < 2 characters long 1151s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '9' because it was < 2 characters long 1151s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '12' because it was < 2 characters long 1151s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '14' because it was < 2 characters long 1151s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '15' because it was < 2 characters long 1151s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '18' because it was < 2 characters long 1151s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '19' because it was < 2 characters long 1151s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '22' because it was < 2 characters long 1151s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '26' because it was < 2 characters long 1151s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '33' because it was < 2 characters long 1151s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '35' because it was < 2 characters long 1151s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '49' because it was < 2 characters long 1151s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '50' because it was < 2 characters long 1151s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 1151s Warning: skipping read '52' because it was < 2 characters long 1151s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '61' because it was < 2 characters long 1151s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '64' because it was < 2 characters long 1151s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '68' because it was < 2 characters long 1151s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '75' because it was < 2 characters long 1151s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '81' because it was < 2 characters long 1151s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '84' because it was < 2 characters long 1151s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '91' because it was < 2 characters long 1151s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '93' because it was < 2 characters long 1151s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '94' because it was < 2 characters long 1151s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '98' because it was < 2 characters long 1151s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '104' because it was < 2 characters long 1151s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '110' because it was < 2 characters long 1151s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '113' because it was < 2 characters long 1151s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '115' because it was < 2 characters long 1151s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '116' because it was < 2 characters long 1151s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '118' because it was < 2 characters long 1151s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '120' because it was < 2 characters long 1151s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '124' because it was < 2 characters long 1151s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '129' because it was < 2 characters long 1151s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 1151s Warning: skipping read '131' because it was < 2 characters long 1151s Warning: skipping read '133' because length (1) <= # seed mismatches (0) 1151s Warning: skipping read '133' because it was < 2 characters long 1151s 140 reads; of these: 1151s 140 (100.00%) were unpaired; of these: 1151s 140 (100.00%) aligned 0 times 1151s 0 (0.00%) aligned exactly 1 time 1151s 0 (0.00%) aligned >1 times 1151s 0.00% overall alignment rate 1151s Read 50 alignments... 1151s Read 100 alignments... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s --- Summary --- 1151s Read 1 reference strings 1151s Checked 0 alignments, 0 edits 1151s --------------- 1151s PASSED 1151s Flattened IUPAC characters 1151s Mutating sequence Sim.pm.2 1151s Introducing 11 SNPs, 0/4 ref/read gaps, and 3 rearrangements 1151s Finished SNPs 1151s Finished ref gaps 1151s Finished read gaps 1151s Mutating sequence Sim.pm.1 1151s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1151s Finished SNPs 1151s Finished ref gaps 1151s Finished read gaps 1151s Mutated reference genome to subject genome 1151s SNPs introduced: 12 1151s Reference gaps introduced: 1 1151s Read gaps introduced: 5 1151s Rearrangements introduced: 3 1151s Created read sampler 1151s Sampling 110 reads 1151s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1151s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1151s parsing sequence Sim.pm.1... 1151s parsing sequence Sim.pm.2... 1151s Parsed 269 reference bases 1151s *** Run 54 of 100 1151s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 7 --large-index --mp 4.66247064867523,1.54381962177561 -a --local -R 4 --norc --score-min L,7.98626602712675,3.39417025004722 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1151s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 1151s Warning: skipping mate #2 of read '5' because it was < 2 characters long 1151s Read 50 alignments... 1151s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 1151s Warning: skipping mate #2 of read '86' because it was < 2 characters long 1151s Warning: skipping mate #2 of read '110' because length (1) <= # seed mismatches (0) 1151s Warning: skipping mate #2 of read '110' because it was < 2 characters long 1151s Read 100 alignments... 1151s 110 reads; of these: 1151s 110 (100.00%) were paired; of these: 1151s 110 (100.00%) aligned concordantly 0 times 1151s 0 (0.00%) aligned concordantly exactly 1 time 1151s 0 (0.00%) aligned concordantly >1 times 1151s ---- 1151s 110 pairs aligned concordantly 0 times; of these: 1151s 0 (0.00%) aligned discordantly 1 time 1151s ---- 1151s 110 pairs aligned 0 times concordantly or discordantly; of these: 1151s 220 mates make up the pairs; of these: 1151s 220 (100.00%) aligned 0 times 1151s 0 (0.00%) aligned exactly 1 time 1151s 0 (0.00%) aligned >1 times 1151s 0.00% overall alignment rate 1151s Read 150 alignments... 1151s Read 200 alignments... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing 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line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s Processing line... 1151s --- Summary --- 1151s Read 1 reference strings 1151s Checked 0 alignments, 0 edits 1151s --------------- 1151s PASSED 1151s ALSO checking that bowtie2 and bowtie2-align match up 1151s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 7 --large-index --mp 4.66247064867523,1.54381962177561 -a --local -R 4 --norc --score-min L,7.98626602712675,3.39417025004722 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1151s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 1151s Warning: skipping mate #2 of read '5' because it was < 2 characters long 1151s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 1151s Warning: skipping mate #2 of read '86' because it was < 2 characters long 1151s Warning: skipping mate #2 of read '110' because length (1) <= # seed mismatches (0) 1151s Warning: skipping mate #2 of read '110' because it was < 2 characters long 1152s 110 reads; of these: 1152s 110 (100.00%) were paired; of these: 1152s 110 (100.00%) aligned concordantly 0 times 1152s 0 (0.00%) aligned concordantly exactly 1 time 1152s 0 (0.00%) aligned concordantly >1 times 1152s ---- 1152s 110 pairs aligned concordantly 0 times; of these: 1152s 0 (0.00%) aligned discordantly 1 time 1152s ---- 1152s 110 pairs aligned 0 times concordantly or discordantly; of these: 1152s 220 mates make up the pairs; of these: 1152s 220 (100.00%) aligned 0 times 1152s 0 (0.00%) aligned exactly 1 time 1152s 0 (0.00%) aligned >1 times 1152s 0.00% overall alignment rate 1152s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1152s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1152s /usr/bin/bowtie2 --mm --cp-ival 1 --cp-min 7 --large-index --mp 4.66247064867523,1.54381962177561 -a --local -R 4 --norc --score-min L,7.98626602712675,3.39417025004722 -f -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1152s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 1152s Warning: skipping mate #2 of read '5' because it was < 2 characters long 1152s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 1152s Warning: skipping mate #2 of read '86' because it was < 2 characters long 1152s Warning: skipping mate #2 of read '110' because length (1) <= # seed mismatches (0) 1152s Warning: skipping mate #2 of read '110' because it was < 2 characters long 1152s 110 reads; of these: 1152s 110 (100.00%) were paired; of these: 1152s 110 (100.00%) aligned concordantly 0 times 1152s 0 (0.00%) aligned concordantly exactly 1 time 1152s 0 (0.00%) aligned concordantly >1 times 1152s ---- 1152s 110 pairs aligned concordantly 0 times; of these: 1152s 0 (0.00%) aligned discordantly 1 time 1152s ---- 1152s 110 pairs aligned 0 times concordantly or discordantly; of these: 1152s 220 mates make up the pairs; of these: 1152s 220 (100.00%) aligned 0 times 1152s 0 (0.00%) aligned exactly 1 time 1152s 0 (0.00%) aligned >1 times 1152s 0.00% overall alignment rate 1152s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1152s Flattened IUPAC characters 1152s Mutating sequence Sim.pm.2 1152s Introducing 33 SNPs, 0/3 ref/read gaps, and 1 rearrangements 1152s Finished SNPs 1152s Finished ref gaps 1152s Finished read gaps 1152s Mutating sequence Sim.pm.1 1152s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1152s Finished SNPs 1152s Finished ref gaps 1152s Finished read gaps 1152s Mutated reference genome to subject genome 1152s SNPs introduced: 35 1152s Reference gaps introduced: 0 1152s Read gaps introduced: 3 1152s Rearrangements introduced: 1 1152s Created read sampler 1152s Sampling 89 reads 1152s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1152s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1152s parsing sequence Sim.pm.1... 1152s parsing sequence Sim.pm.2... 1152s Parsed 269 reference bases 1152s *** Run 55 of 100 1152s /usr/bin/bowtie2 --np 3 -N 1 -L14 --rfg 47.6075937778901 --score-min L,2.15089780037585,7.40419774705396 --cp-min 3 --cp-ival 5 --mm --trim3 9 --rdg 32.9311921052408,1.36143913386498 --large-index -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1152s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '3' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1152s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '6' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1152s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '8' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1152s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '11' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1152s Warning: skipping read '13' because length (1) <= # seed mismatches (1) 1152s Warning: skipping read '13' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1152s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '16' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1152s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '17' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1152s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '28' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1152s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '29' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1152s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '33' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1152s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '35' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1152s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '39' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1152s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '40' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1152s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '42' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1152s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '43' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1152s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '45' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1152s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '52' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1152s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '56' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1152s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '59' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1152s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '62' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1152s Warning: skipping read '63' because length (1) <= # seed mismatches (1) 1152s Warning: skipping read '63' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1152s Warning: skipping read '66' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '66' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1152s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '68' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1152s Warning: skipping read '72' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '72' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1152s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '77' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1152s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '80' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1152s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '82' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1152s 89 reads; of these: 1152s 89 (100.00%) were unpaired; of these: 1152s 77 (86.52%) aligned 0 times 1152s 2 (2.25%) aligned exactly 1 time 1152s 10 (11.24%) aligned >1 times 1152s 13.48% overall alignment rate 1152s Read 50 alignments... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s TCACATCG 1152s TCACATCG 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s CAAA 1152s CAAA 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s ACGA 1152s ACGA 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s GGCTGAAGT 1152s GGCTGAAGT 1152s Processing line... 1152s CTCGTGGG 1152s CTCGTGGG 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s AC 1152s AC 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s TCGTGG 1152s TCGTGG 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s CGAGCCTGTCACATCGAGATG 1152s CGAGCCTGTCACATCGAGATG 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s AGATGGACCACCT 1152s AGATGGACCACCT 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s CACATCGA 1152s CACATCGA 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s GG 1152s GG 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s AGCCTGTCACATCGAGA 1152s AGCCTGTCACATCGAGA 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s Processing line... 1152s --- Summary --- 1152s Read 1 reference strings 1152s Checked 12 alignments, 0 edits 1152s --------------- 1152s PASSED 1152s ALSO checking that bowtie2 and bowtie2-align match up 1152s /usr/bin/bowtie2 --np 3 -N 1 -L14 --rfg 47.6075937778901 --score-min L,2.15089780037585,7.40419774705396 --cp-min 3 --cp-ival 5 --mm --trim3 9 --rdg 32.9311921052408,1.36143913386498 --large-index -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1152s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '3' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1152s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '6' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1152s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '8' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1152s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '11' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1152s Warning: skipping read '13' because length (1) <= # seed mismatches (1) 1152s Warning: skipping read '13' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1152s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '16' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1152s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '17' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1152s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '28' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1152s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '29' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1152s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '33' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1152s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '35' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1152s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '39' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1152s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '40' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1152s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '42' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1152s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '43' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1152s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '45' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1152s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '52' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1152s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '56' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1152s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '59' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1152s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '62' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1152s Warning: skipping read '63' because length (1) <= # seed mismatches (1) 1152s Warning: skipping read '63' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1152s Warning: skipping read '66' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '66' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1152s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '68' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1152s Warning: skipping read '72' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '72' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1152s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '77' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1152s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '80' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1152s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '82' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1152s 89 reads; of these: 1152s 89 (100.00%) were unpaired; of these: 1152s 77 (86.52%) aligned 0 times 1152s 2 (2.25%) aligned exactly 1 time 1152s 10 (11.24%) aligned >1 times 1152s 13.48% overall alignment rate 1152s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1152s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1152s /usr/bin/bowtie2 --np 3 -N 1 -L14 --rfg 47.6075937778901 --score-min L,2.15089780037585,7.40419774705396 --cp-min 3 --cp-ival 5 --mm --trim3 9 --rdg 32.9311921052408,1.36143913386498 --large-index -f -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1152s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '3' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1152s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '6' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1152s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '8' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1152s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '11' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1152s Warning: skipping read '13' because length (1) <= # seed mismatches (1) 1152s Warning: skipping read '13' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1152s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '16' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1152s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '33' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1152s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '35' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1152s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '17' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1152s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '39' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1152s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '40' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1152s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '42' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1152s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '43' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1152s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '45' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1152s Warning: skipping read '66' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '66' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1152s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 1152s Warning: skipping read '68' because it was < 2 characters long 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1152s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1153s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 1153s Warning: skipping read '82' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1153s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 1153s Warning: skipping read '28' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1153s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1153s Warning: skipping read '29' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1153s Warning: skipping read '72' because length (0) <= # seed mismatches (1) 1153s Warning: skipping read '72' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1153s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 1153s Warning: skipping read '77' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1153s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1153s Warning: skipping read '80' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1153s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 1153s Warning: skipping read '52' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1153s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 1153s Warning: skipping read '56' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1153s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 1153s Warning: skipping read '59' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1153s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 1153s Warning: skipping read '62' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1153s Warning: skipping read '63' because length (1) <= # seed mismatches (1) 1153s Warning: skipping read '63' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1153s 89 reads; of these: 1153s 89 (100.00%) were unpaired; of these: 1153s 77 (86.52%) aligned 0 times 1153s 2 (2.25%) aligned exactly 1 time 1153s 10 (11.24%) aligned >1 times 1153s 13.48% overall alignment rate 1153s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1153s Flattened IUPAC characters 1153s Mutating sequence Sim.pm.2 1153s Introducing 33 SNPs, 4/1 ref/read gaps, and 0 rearrangements 1153s Finished SNPs 1153s Finished ref gaps 1153s Finished read gaps 1153s Mutating sequence Sim.pm.1 1153s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1153s Finished SNPs 1153s Finished ref gaps 1153s Finished read gaps 1153s Mutated reference genome to subject genome 1153s SNPs introduced: 39 1153s Reference gaps introduced: 4 1153s Read gaps introduced: 2 1153s Rearrangements introduced: 1 1153s Created read sampler 1153s Sampling 41 reads 1153s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1153s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1153s parsing sequence Sim.pm.1... 1153s parsing sequence Sim.pm.2... 1153s Parsed 269 reference bases 1153s *** Run 56 of 100 1153s /usr/bin/bowtie2 --rdg 4.84338805530592,19.6867310257499 --mp 8.75067504067318,7.46933909733492 --local --large-index --score-min L,7.86120786760127,9.48999074317944 -k 4 --cp-min 11 --np 2 --cp-ival 1 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1153s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 1153s Warning: skipping read '32' because it was < 2 characters long 1153s 41 reads; of these: 1153s 41 (100.00%) were unpaired; of these: 1153s 41 (100.00%) aligned 0 times 1153s 0 (0.00%) aligned exactly 1 time 1153s 0 (0.00%) aligned >1 times 1153s 0.00% overall alignment rate 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s --- Summary --- 1153s Read 1 reference strings 1153s Checked 0 alignments, 0 edits 1153s --------------- 1153s PASSED 1153s Flattened IUPAC characters 1153s Mutating sequence Sim.pm.1 1153s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1153s Finished SNPs 1153s Finished ref gaps 1153s Finished read gaps 1153s Mutating sequence Sim.pm.2 1153s Introducing 10 SNPs, 1/0 ref/read gaps, and 2 rearrangements 1153s Finished SNPs 1153s Finished ref gaps 1153s Finished read gaps 1153s Mutated reference genome to subject genome 1153s SNPs introduced: 10 1153s Reference gaps introduced: 2 1153s Read gaps introduced: 0 1153s Rearrangements introduced: 2 1153s Created read sampler 1153s Sampling 44 reads 1153s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1153s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1153s parsing sequence Sim.pm.1... 1153s parsing sequence Sim.pm.2... 1153s Parsed 269 reference bases 1153s *** Run 57 of 100 1153s /usr/bin/bowtie2 --cp-min 2 --mm --cp-ival 2 --trim3 7 --mp 7.16940661538372,2.28508055034645 -a --large-index --norc --nofw --np 1 -R 1 --rfg 24.4938265383128,1.76487594145092 --score-min L,4.73313821308163,1.58738191236158 -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1153s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1153s Warning: skipping read '19' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1153s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1153s Warning: skipping read '23' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1153s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 1153s Warning: skipping read '28' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1153s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1153s Warning: skipping read '29' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1153s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1153s Warning: skipping read '30' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1153s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1153s Warning: skipping read '31' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1153s 44 reads; of these: 1153s 44 (100.00%) were unpaired; of these: 1153s 44 (100.00%) aligned 0 times 1153s 0 (0.00%) aligned exactly 1 time 1153s 0 (0.00%) aligned >1 times 1153s 0.00% overall alignment rate 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s /usr/bin/bowtie2 --cp-min 2 --mm --cp-ival 2 --trim3 7 --mp 7.16940661538372,2.28508055034645 -a --large-index --norc --nofw --np 1 -R 1 --rfg 24.4938265383128,1.76487594145092 --score-min L,4.73313821308163,1.58738191236158 -r -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s Processing line... 1153s --- Summary --- 1153s Read 1 reference strings 1153s Checked 0 alignments, 0 edits 1153s --------------- 1153s PASSED 1153s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1153s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1153s Warning: skipping read '19' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1153s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1153s Warning: skipping read '23' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1153s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 1153s Warning: skipping read '28' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1153s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1153s Warning: skipping read '29' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1153s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1153s Warning: skipping read '30' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1153s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1153s Warning: skipping read '31' because it was < 2 characters long 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1153s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1153s 44 reads; of these: 1153s 44 (100.00%) were unpaired; of these: 1153s 44 (100.00%) aligned 0 times 1153s 0 (0.00%) aligned exactly 1 time 1153s 0 (0.00%) aligned >1 times 1153s 0.00% overall alignment rate 1153s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1153s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1153s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1153s /usr/bin/bowtie2 --cp-min 2 --mm --cp-ival 2 --trim3 7 --mp 7.16940661538372,2.28508055034645 -a --large-index --norc --nofw --np 1 -R 1 --rfg 24.4938265383128,1.76487594145092 --score-min L,4.73313821308163,1.58738191236158 -r -p 2 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1153s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1154s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 1154s Warning: skipping read '19' because it was < 2 characters long 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1154s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1154s Warning: skipping read '23' because it was < 2 characters long 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1154s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 1154s Warning: skipping read '28' because it was < 2 characters long 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1154s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 1154s Warning: skipping read '29' because it was < 2 characters long 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1154s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1154s Warning: skipping read '30' because it was < 2 characters long 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1154s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 1154s Warning: skipping read '31' because it was < 2 characters long 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1154s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1154s 44 reads; of these: 1154s 44 (100.00%) were unpaired; of these: 1154s 44 (100.00%) aligned 0 times 1154s 0 (0.00%) aligned exactly 1 time 1154s 0 (0.00%) aligned >1 times 1154s 0.00% overall alignment rate 1154s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1154s Flattened IUPAC characters 1154s Mutating sequence Sim.pm.2 1154s Introducing 4 SNPs, 2/1 ref/read gaps, and 4 rearrangements 1154s Finished SNPs 1154s Finished ref gaps 1154s Finished read gaps 1154s Mutating sequence Sim.pm.1 1154s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1154s Finished SNPs 1154s Finished ref gaps 1154s Finished read gaps 1154s Mutated reference genome to subject genome 1154s SNPs introduced: 4 1154s Reference gaps introduced: 2 1154s Read gaps introduced: 1 1154s Rearrangements introduced: 4 1154s Created read sampler 1154s Sampling 45 reads 1154s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1154s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1154s parsing sequence Sim.pm.1... 1154s parsing sequence Sim.pm.2... 1154s Parsed 269 reference bases 1154s *** Run 58 of 100 1154s /usr/bin/bowtie2 -a --local --large-index --gbar 1 --score-min L,3.91030429367715,1.28004828086314 --cp-min 3 --np 4 --mm --cp-ival 3 -D 23 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1154s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 1154s Warning: skipping read '13' because it was < 2 characters long 1154s 45 reads; of these: 1154s 45 (100.00%) were unpaired; of these: 1154s 20 (44.44%) aligned 0 times 1154s 7 (15.56%) aligned exactly 1 time 1154s 18 (40.00%) aligned >1 times 1154s 55.56% overall alignment rate 1154s Read 50 alignments... 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s TCGAGATGGACCACCT 1154s TCGAGATGGACCACCT 1154s Processing line... 1154s TCGAGATGGACCACCT 1154s TCGAGATGGACCACCT 1154s Processing line... 1154s TCGAGATGGACCACCT 1154s TCGAGATGGACCACCT 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s TGGAT 1154s TGGAT 1154s Processing line... 1154s TGGAT 1154s TGGAT 1154s Processing line... 1154s TGGAT 1154s TGGAT 1154s Processing line... 1154s CGAGCCTGTCACATCGAGATGGACCACCTC 1154s CGAGCCTGTCACATCGAGATGGACCACCTC 1154s Processing line... 1154s CGAGCCTGTCACATCGAGATGGACCACCTC 1154s CGAGCCTGTCACATCGAGATGGACCACCTC 1154s Processing line... 1154s CGAGCCTGTCACATCGAGATGGACCACCTC 1154s CGAGCCTGTCACATCGAGATGGACCACCTC 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s CACATCGAGATGGACCACCTCGTAGGATGGATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGG 1154s CACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGAT-G 1154s Processing line... 1154s CACATCGAGATGGACCACCTCGTAGGATGGATAACCACAGTAGAACACGAGCCTGTCACATCGAGATGG 1154s CACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGAT-G 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s GGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGG 1154s GGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGAT-G 1154s Processing line... 1154s GGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACC 1154s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGA-C 1154s Processing line... 1154s AGCTCGCAGCGCG 1154s AGCTCGCAGCGCG 1154s Processing line... 1154s GCCTGTCACATCGAGATGGACCACCTCGTG 1154s GCCTGTCACATCGAGATGGACCACCTCGTG 1154s Processing line... 1154s GCCTGTCACATCGAGATGGACCACCTCGTG 1154s GCCTGTCACATCGAGATGGACCACCTCGTG 1154s Processing line... 1154s GCCTGTCACATCGAGATGGACCACCTCGTG 1154s GCCTGTCACATCGAGATGGACCACCTCGTG 1154s Processing line... 1154s CATCGAGATGGACCACCTCGACGAGCTGGGTTGGATAACCATAGTATAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAAC 1154s CATCGAGATGGACCACCTCG------TGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAAC 1154s Processing line... 1154s CATCGAGATGGACCACCTCGACGAGCTGGGTTGGATAACCATAGTATAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAAC 1154s CATCGAGATGGACCACCTCG------TGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAAC 1154s Processing line... 1154s Processing line... 1154s AACCAAAACGCTGAAATTAGAGCTCGCAGCGCGT-A 1154s AACCAAAACGCNGAAATTAGAGCTCGCAGCGCGTAA 1154s Processing line... 1154s GTGGG 1154s GTGGG 1154s Processing line... 1154s GTGGG 1154s GTGGG 1154s Processing line... 1154s GTGGG 1154s GTGGG 1154s Processing line... 1154s GCTCGCAGCG 1154s GCTCGCAGCG 1154s Processing line... 1154s Processing line... 1154s ATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGG--T--A 1154s ATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGA 1154s Processing line... 1154s ATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGG--T--A 1154s ATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGA 1154s Processing line... 1154s GGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGG 1154s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGG 1154s Processing line... 1154s ACATCGAGATGGACCACCTCGTGGGCTGGATAACCAAAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGG 1154s ACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGAT-G 1154s Processing line... 1154s GGATAACCAAAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACC 1154s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCA-C 1154s Processing line... 1154s Processing line... 1154s ACGAGCCTGTCACATCGAGATGGACCACCTCGACGAGCTGGGTTGGATAACCATAGTATAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGG 1154s ACGAGCCTGTCACATCGAGATGGACCACCTCG------TGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGT-GG 1154s Processing line... 1154s ACGAGCCTGTCACATCGAGATGGACCACCTCGACGAGCTGGGTTGGATAACCATAGTATAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGG 1154s ACGAGCCTGTCACATCGAGATGGACCACCTCG------TGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGT-GG 1154s Processing line... 1154s Processing line... 1154s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGACGAGCTGGGTTGGATAACCATAGTATAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGG 1154s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCG------TGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGT-GG 1154s Processing line... 1154s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGACGAGCTGGGTTGGATAACCATAGTATAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGG 1154s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCG------TGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGT-GG 1154s Processing line... 1154s ATAAC 1154s ATAAC 1154s Processing line... 1154s ATAAC 1154s ATAAC 1154s Processing line... 1154s ATAAC 1154s ATAAC 1154s Processing line... 1154s ATAAC 1154s ATAAC 1154s Processing line... 1154s Processing line... 1154s GATAACCAGAGTAGAACACGAGCCTGTCACATC--G 1154s GATAACCANAGTAGAACACGAGCCTGTCACATCGAG 1154s Processing line... 1154s GATAACCAGAGTAGAACACGAGCCTGTCACATC--G 1154s GATAACCANAGTAGAACACGAGCCTGTCACATCGAG 1154s Processing line... 1154s GATAACCAGAGTAGAACACGAGCCTGTCACATC--G 1154s GATAACCANAGTAGAACACGAGCCTGTCACATCGAG 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s Processing line... 1154s GATAACCATAGTAGAACAC--GCCTGTCACATCGAGATGGACCACCTCGTAGGATGGATAACC 1154s GATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACC 1154s Processing line... 1154s GATAACCATAGTAGAACAC--GCCTGTCACATCGAGATGGACCACCTCGTAGGATGGATAACC 1154s GATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACC 1154s Processing line... 1154s GATAACCATAGTAGAACAC--GCCTGTCACATCGAGATGGACCACCTCGTAGGATGGATAACCACA 1154s GATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAA 1154s Processing line... 1154s Processing line... 1154s ACCACCTCGTGGGGTGGATAACCAAAACGCTGAAATTAGAGCTCGCAGCGC 1154s ACCACCTCGTGGGNTGGATAACCAAAACGCNGAAATTAGAGCTCGCA--GC 1154s Processing line... 1154s ACCACCTCGTGGGGTGGATAACCAAAACGCTGAAATTAGAGCTCGCAGCGCGTA--AG 1154s ACCACCTCGTGGGNTGGATAACCAAAACGCNGAAATTAGAGCTCGCAGCGCGTAANAG 1154s Processing line... 1154s CCTGTCACATCGAGATGGACCACCTCGT 1154s CCTGTCACATCGAGATGGACCACCTCGT 1154s Processing line... 1154s CCTGTCACATCGAGATGGACCACCTCGT 1154s CCTGTCACATCGAGATGGACCACCTCGT 1154s Processing line... 1154s CCTGTCACATCGAGATGGACCACCTCGT 1154s CCTGTCACATCGAGATGGACCACCTCGT 1154s Processing line... 1154s CCACCTCGTGGGGTGGATAACCAAAACGCTGAAATTAGAGCTCGCAGCGCGTAAGCAGGGCGGGGTATGGTGAGGGTCGAGGACC 1154s CCACCTCGTGGGNTGGATAACCAAAACGCNGAAATTAGAGCTCGCAGCGCGTAA-NAGGGNGGGGTATGGTGAGGGTCGAGGA-C 1154s Processing line... 1154s Processing line... 1154s GAGCTCGCAGC 1154s GAGCTCGCAGC 1154s Processing line... 1154s GAACACGAGCCTGTCACATCGAGATG 1154s GAACACGAGCCTGTCACATCGAGATG 1154s Processing line... 1154s GAACACGAGCCTGTCACATCGAGATG 1154s GAACACGAGCCTGTCACATCGAGATG 1154s Processing line... 1154s GAACACGAGCCTGTCACATCGAGATG 1154s GAACACGAGCCTGTCACATCGAGATG 1154s Processing line... 1154s CCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGA 1154s CCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACC--A 1154s Processing line... 1154s CCACCTCGTGGGGTGGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTA 1154s CCACCTCGTGGGNTGGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCAAA--A 1154s Processing line... 1154s GGATAACCAGAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGGTGGATAACCAGAGTAGA--AC 1154s GGATAACCANAGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAACAC 1154s --- Summary --- 1154s Read 1 reference strings 1154s Checked 56 alignments, 0 edits 1154s --------------- 1154s PASSED 1154s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1154s /usr/bin/bowtie2 -a --local --large-index --gbar 1 --score-min L,3.91030429367715,1.28004828086314 --cp-min 3 --np 4 --mm --cp-ival 3 -D 23 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1154s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 1154s Warning: skipping read '13' because it was < 2 characters long 1154s 45 reads; of these: 1154s 45 (100.00%) were unpaired; of these: 1154s 20 (44.44%) aligned 0 times 1154s 7 (15.56%) aligned exactly 1 time 1154s 18 (40.00%) aligned >1 times 1154s 55.56% overall alignment rate 1154s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1154s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1154s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1154s Flattened IUPAC characters 1154s Mutating sequence Sim.pm.2 1154s Introducing 22 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1154s Finished SNPs 1154s Finished ref gaps 1154s Finished read gaps 1154s Mutating sequence Sim.pm.1 1154s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1154s Finished SNPs 1154s Finished ref gaps 1154s Finished read gaps 1154s Mutated reference genome to subject genome 1154s SNPs introduced: 22 1154s Reference gaps introduced: 1 1154s Read gaps introduced: 2 1154s Rearrangements introduced: 1 1154s Created read sampler 1154s Sampling 15 reads 1154s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1154s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1154s parsing sequence Sim.pm.1... 1154s parsing sequence Sim.pm.2... 1154s Parsed 269 reference bases 1154s *** Run 59 of 100 1154s /usr/bin/bowtie2 --cp-min 2 -N 0 -L25 --cp-ival 3 --mp 5.00989490786617,3.66108524482336 --trim3 6 --trim5 4 --rfg 11.446911562694,19.3568926417902 --large-index --score-min L,3.63871513460334,9.94040055895879 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq 1154s 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 1154s 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 1154s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 1154s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 1154s 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 1154s 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 1154s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1154s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1154s 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 1154s 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 1154s 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 1154s 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 1154s 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 1154s 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 1154s 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 1154s 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 1154s 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 1154s 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 1154s 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 1154s 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 1154s 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 1155s 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 1155s 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 1155s 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 1155s 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 1155s 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 1155s 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 1155s 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 1155s 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 1155s 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 1155s 15 reads; of these: 1155s 11 (73.33%) were paired; of these: 1155s 11 (100.00%) aligned concordantly 0 times 1155s 0 (0.00%) aligned concordantly exactly 1 time 1155s 0 (0.00%) aligned concordantly >1 times 1155s ---- 1155s 11 pairs aligned concordantly 0 times; of these: 1155s 0 (0.00%) aligned discordantly 1 time 1155s ---- 1155s 11 pairs aligned 0 times concordantly or discordantly; of these: 1155s 22 mates make up the pairs; of these: 1155s 19 (86.36%) aligned 0 times 1155s 0 (0.00%) aligned exactly 1 time 1155s 3 (13.64%) aligned >1 times 1155s 4 (26.67%) were unpaired; of these: 1155s 3 (75.00%) aligned 0 times 1155s 0 (0.00%) aligned exactly 1 time 1155s 1 (25.00%) aligned >1 times 1155s 15.38% overall alignment rate 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s GGATAACC 1155s GGATAACC 1155s Processing line... 1155s Processing line... 1155s GTGGG 1155s GTGGG 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s AT 1155s AT 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s CACCTC 1155s CACCTC 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s --- Summary --- 1155s Read 1 reference strings 1155s Checked 4 alignments, 0 edits 1155s --------------- 1155s PASSED 1155s Flattened IUPAC characters 1155s Mutating sequence Sim.pm.2 1155s Introducing 10 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1155s Finished SNPs 1155s Finished ref gaps 1155s Finished read gaps 1155s Mutating sequence Sim.pm.1 1155s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1155s Finished SNPs 1155s Finished ref gaps 1155s Finished read gaps 1155s Mutated reference genome to subject genome 1155s SNPs introduced: 12 1155s Reference gaps introduced: 0 1155s Read gaps introduced: 0 1155s Rearrangements introduced: 2 1155s Created read sampler 1155s Sampling 32 reads 1155s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1155s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1155s parsing sequence Sim.pm.1... 1155s *** Run 60 of 100 1155s /usr/bin/bowtie2 --cp-ival 4 --cp-min 7 --large-index -k 4 --trim3 6 --local -R 1 -D 47 --nofw --score-min L,5.49640961372984,4.8374449881645 --rfg 30.1395917725122 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1155s parsing sequence Sim.pm.2... 1155s Parsed 269 reference bases 1155s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1155s Warning: skipping read '3' because it was < 2 characters long 1155s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1155s Warning: skipping read '6' because it was < 2 characters long 1155s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1155s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1155s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1155s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1155s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1155s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1155s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 1155s Warning: skipping read '28' because it was < 2 characters long 1155s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1155s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1155s 32 reads; of these: 1155s 26 (81.25%) were paired; of these: 1155s 26 (100.00%) aligned concordantly 0 times 1155s 0 (0.00%) aligned concordantly exactly 1 time 1155s 0 (0.00%) aligned concordantly >1 times 1155s ---- 1155s 26 pairs aligned concordantly 0 times; of these: 1155s 0 (0.00%) aligned discordantly 1 time 1155s ---- 1155s 26 pairs aligned 0 times concordantly or discordantly; of these: 1155s 52 mates make up the pairs; of these: 1155s 52 (100.00%) aligned 0 times 1155s 0 (0.00%) aligned exactly 1 time 1155s 0 (0.00%) aligned >1 times 1155s 6 (18.75%) were unpaired; of these: 1155s 6 (100.00%) aligned 0 times 1155s 0 (0.00%) aligned exactly 1 time 1155s 0 (0.00%) aligned >1 times 1155s 0.00% overall alignment rate 1155s Read 50 alignments... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s --- Summary --- 1155s Read 1 reference strings 1155s Checked 0 alignments, 0 edits 1155s --------------- 1155s PASSED 1155s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1155s /usr/bin/bowtie2 --cp-ival 4 --cp-min 7 --large-index -k 4 --trim3 6 --local -R 1 -D 47 --nofw --score-min L,5.49640961372984,4.8374449881645 --rfg 30.1395917725122 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1155s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 1155s Warning: skipping read '3' because it was < 2 characters long 1155s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1155s Warning: skipping read '6' because it was < 2 characters long 1155s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 1155s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1155s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 1155s Warning: skipping mate #1 of read '15' because it was < 2 characters long 1155s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1155s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1155s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 1155s Warning: skipping read '28' because it was < 2 characters long 1155s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1155s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1155s 32 reads; of these: 1155s 26 (81.25%) were paired; of these: 1155s 26 (100.00%) aligned concordantly 0 times 1155s 0 (0.00%) aligned concordantly exactly 1 time 1155s 0 (0.00%) aligned concordantly >1 times 1155s ---- 1155s 26 pairs aligned concordantly 0 times; of these: 1155s 0 (0.00%) aligned discordantly 1 time 1155s ---- 1155s 26 pairs aligned 0 times concordantly or discordantly; of these: 1155s 52 mates make up the pairs; of these: 1155s 52 (100.00%) aligned 0 times 1155s 0 (0.00%) aligned exactly 1 time 1155s 0 (0.00%) aligned >1 times 1155s 6 (18.75%) were unpaired; of these: 1155s 6 (100.00%) aligned 0 times 1155s 0 (0.00%) aligned exactly 1 time 1155s 0 (0.00%) aligned >1 times 1155s 0.00% overall alignment rate 1155s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1155s Flattened IUPAC characters 1155s Mutating sequence Sim.pm.1 1155s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1155s Finished SNPs 1155s Finished ref gaps 1155s Finished read gaps 1155s Mutating sequence Sim.pm.2 1155s Introducing 20 SNPs, 2/2 ref/read gaps, and 6 rearrangements 1155s Finished SNPs 1155s Finished ref gaps 1155s Finished read gaps 1155s Mutated reference genome to subject genome 1155s SNPs introduced: 23 1155s Reference gaps introduced: 3 1155s Read gaps introduced: 3 1155s Rearrangements introduced: 6 1155s Created read sampler 1155s Sampling 130 reads 1155s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1155s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1155s parsing sequence Sim.pm.1... 1155s parsing sequence Sim.pm.2... 1155s Parsed 269 reference bases 1155s *** Run 61 of 100 1155s /usr/bin/bowtie2 -R 4 -N 1 -L27 --np 3 --score-min L,5.96708956696215,2.19064243566459 --n-ceil 0.284313731671622,0.647458892797123 --rfg 26.336975497493,9.74135150993936 --cp-ival 2 --cp-min 6 --large-index --rdg 4.28383795270986 --trim3 6 --mp 9.35411391411893,4.515760096181 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1155s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '2' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1155s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '5' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1155s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '6' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1155s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '7' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1155s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '9' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1155s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '12' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1155s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '15' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1155s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '19' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1155s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '24' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1155s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '25' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1155s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '27' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1155s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '29' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1155s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '34' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1155s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '35' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1155s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '39' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1155s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '42' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1155s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '55' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1155s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '57' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1155s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '80' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1155s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '88' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1155s Warning: skipping read '89' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '89' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1155s Warning: skipping read '92' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '92' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1155s Warning: skipping read '106' because length (1) <= # seed mismatches (1) 1155s Warning: skipping read '106' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1155s Warning: skipping read '110' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '110' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1155s Warning: skipping read '111' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '111' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1155s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '119' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1155s Warning: skipping read '121' because length (1) <= # seed mismatches (1) 1155s Warning: skipping read '121' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1155s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '125' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1155s Warning: skipping read '128' because length (0) <= # seed mismatches (1) 1155s Warning: skipping read '128' because it was < 2 characters long 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1155s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1155s 130 reads; of these: 1155s 130 (100.00%) were unpaired; of these: 1155s 111 (85.38%) aligned 0 times 1155s 0 (0.00%) aligned exactly 1 time 1155s 19 (14.62%) aligned >1 times 1155s 14.62% overall alignment rate 1155s Read 50 alignments... 1155s Read 100 alignments... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s AGAACAC 1155s AGAACAC 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s CACCT 1155s CACCT 1155s Processing line... 1155s Processing line... 1155s CATCGAGATGGA 1155s CATCGAGATGGA 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s GG 1155s GG 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s GGACC 1155s GGACC 1155s Processing line... 1155s ACG 1155s ACG 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s GAGATGG 1155s GAGATGG 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s GGA 1155s GGA 1155s Processing line... 1155s CGAGCCTG 1155s CGAGCCTG 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s ATGG 1155s ATGG 1155s Processing line... 1155s Processing line... 1155s TGGATAACCA 1155s TGGATAACCA 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s /usr/bin/bowtie2 -R 4 -N 1 -L27 --np 3 --score-min L,5.96708956696215,2.19064243566459 --n-ceil 0.284313731671622,0.647458892797123 --rfg 26.336975497493,9.74135150993936 --cp-ival 2 --cp-min 6 --large-index --rdg 4.28383795270986 --trim3 6 --mp 9.35411391411893,4.515760096181 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1155s Processing line... 1155s Processing line... 1155s TAGAACAC 1155s TAGAACAC 1155s Processing line... 1155s Processing line... 1155s CACCT 1155s CACCT 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s CACCTCGTGG 1155s CACCTCGTGG 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s AGAACACG 1155s AGAACACG 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s AGAACACGAGCCTGTCACATCGA 1155s AGAACACGAGCCTGTCACATCGA 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s TGTC 1155s TGTC 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s GT 1155s GT 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s AGAACACGAGCCTGTCACATCGAGATGGACCACCT 1155s AGAACACGAGCCTGTCACATCGAGATGGACCACCT 1155s Processing line... 1155s Processing line... 1155s Processing line... 1155s --- Summary --- 1155s Read 1 reference strings 1155s Checked 19 alignments, 0 edits 1155s --------------- 1155s PASSED 1155s ALSO checking that bowtie2 and bowtie2-align match up 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1156s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '2' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1156s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '5' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1156s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '6' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1156s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '7' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1156s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '9' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1156s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '12' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1156s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '15' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1156s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '19' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1156s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '24' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1156s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '25' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1156s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '27' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1156s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '29' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1156s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '34' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1156s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '35' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1156s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '39' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1156s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '42' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1156s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '55' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1156s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '57' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1156s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '80' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1156s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '88' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1156s Warning: skipping read '89' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '89' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1156s Warning: skipping read '92' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '92' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1156s Warning: skipping read '106' because length (1) <= # seed mismatches (1) 1156s Warning: skipping read '106' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1156s Warning: skipping read '110' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '110' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1156s Warning: skipping read '111' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '111' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1156s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '119' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1156s Warning: skipping read '121' because length (1) <= # seed mismatches (1) 1156s Warning: skipping read '121' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1156s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '125' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1156s Warning: skipping read '128' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '128' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1156s 130 reads; of these: 1156s 130 (100.00%) were unpaired; of these: 1156s 111 (85.38%) aligned 0 times 1156s 0 (0.00%) aligned exactly 1 time 1156s 19 (14.62%) aligned >1 times 1156s 14.62% overall alignment rate 1156s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1156s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1156s /usr/bin/bowtie2 -R 4 -N 1 -L27 --np 3 --score-min L,5.96708956696215,2.19064243566459 --n-ceil 0.284313731671622,0.647458892797123 --rfg 26.336975497493,9.74135150993936 --cp-ival 2 --cp-min 6 --large-index --rdg 4.28383795270986 --trim3 6 --mp 9.35411391411893,4.515760096181 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1156s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '2' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1156s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '5' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1156s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '6' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1156s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '7' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1156s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '9' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1156s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '12' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1156s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '15' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1156s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '34' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1156s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '35' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1156s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '39' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1156s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '42' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1156s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '19' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1156s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '24' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1156s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '25' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1156s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '27' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1156s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '55' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1156s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '57' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1156s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '80' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1156s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '88' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1156s Warning: skipping read '89' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '89' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1156s Warning: skipping read '92' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '92' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1156s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '29' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1156s Warning: skipping read '106' because length (1) <= # seed mismatches (1) 1156s Warning: skipping read '106' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1156s Warning: skipping read '110' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '110' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1156s Warning: skipping read '111' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '111' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1156s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '119' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1156s Warning: skipping read '121' because length (1) <= # seed mismatches (1) 1156s Warning: skipping read '121' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 1156s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '125' because it was < 2 characters long 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 1156s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 1156s Warning: skipping read '128' because length (0) <= # seed mismatches (1) 1156s Warning: skipping read '128' because it was < 2 characters long 1156s 130 reads; of these: 1156s 130 (100.00%) were unpaired; of these: 1156s 111 (85.38%) aligned 0 times 1156s 0 (0.00%) aligned exactly 1 time 1156s 19 (14.62%) aligned >1 times 1156s 14.62% overall alignment rate 1156s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1156s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1156s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1156s Flattened IUPAC characters 1156s Mutating sequence Sim.pm.1 1156s Introducing 12 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1156s Finished SNPs 1156s Finished ref gaps 1156s Finished read gaps 1156s Mutating sequence Sim.pm.2 1156s Introducing 27 SNPs, 3/2 ref/read gaps, and 7 rearrangements 1156s Finished SNPs 1156s Finished ref gaps 1156s Finished read gaps 1156s Mutated reference genome to subject genome 1156s SNPs introduced: 39 1156s Reference gaps introduced: 3 1156s Read gaps introduced: 2 1156s Rearrangements introduced: 7 1156s Created read sampler 1156s Sampling 67 reads 1156s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1156s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1156s parsing sequence Sim.pm.1... 1156s parsing sequence Sim.pm.2... 1156s Parsed 269 reference bases 1156s *** Run 62 of 100 1156s /usr/bin/bowtie2 --np 9 --score-min L,5.60215668901024,3.51434626091245 --n-ceil 0.142175373427992,0.0762577701741413 --mm --cp-ival 1 --cp-min 4 -M 2 --large-index --local --trim3 8 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq 1156s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1156s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1156s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1156s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1156s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1156s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 1156s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1156s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1156s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1156s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1156s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1156s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1156s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 1156s Read 50 alignments... 1156s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 1156s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1156s 67 reads; of these: 1156s 51 (76.12%) were paired; of these: 1156s 51 (100.00%) aligned concordantly 0 times 1156s 0 (0.00%) aligned concordantly exactly 1 time 1156s 0 (0.00%) aligned concordantly >1 times 1156s ---- 1156s 51 pairs aligned concordantly 0 times; of these: 1156s 0 (0.00%) aligned discordantly 1 time 1156s ---- 1156s 51 pairs aligned 0 times concordantly or discordantly; of these: 1156s 102 mates make up the pairs; of these: 1156s 102 (100.00%) aligned 0 times 1156s 0 (0.00%) aligned exactly 1 time 1156s 0 (0.00%) aligned >1 times 1156s 16 (23.88%) were unpaired; of these: 1156s 16 (100.00%) aligned 0 times 1156s 0 (0.00%) aligned exactly 1 time 1156s 0 (0.00%) aligned >1 times 1156s 0.00% overall alignment rate 1156s Read 100 alignments... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s Processing line... 1156s --- Summary --- 1156s Read 1 reference strings 1156s Checked 0 alignments, 0 edits 1156s --------------- 1156s PASSED 1156s Flattened IUPAC characters 1156s Mutating sequence Sim.pm.1 1156s Introducing 1 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1156s Finished SNPs 1156s Finished ref gaps 1156s Finished read gaps 1156s Mutating sequence Sim.pm.2 1156s Introducing 12 SNPs, 3/2 ref/read gaps, and 1 rearrangements 1156s Finished SNPs 1156s Finished ref gaps 1156s Finished read gaps 1156s Mutated reference genome to subject genome 1156s SNPs introduced: 13 1156s Reference gaps introduced: 3 1156s Read gaps introduced: 2 1156s Rearrangements introduced: 3 1156s Created read sampler 1156s Sampling 53 reads 1156s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1156s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1156s parsing sequence Sim.pm.1... 1156s parsing sequence Sim.pm.2... 1156s Parsed 269 reference bases 1156s *** Run 63 of 100 1156s /usr/bin/bowtie2 --norc --np 1 --nofw --trim5 6 -i C,0.463275115181871 --gbar 3 --score-min L,7.0264014593531,7.91141183183995 --cp-min 4 --cp-ival 3 --rdg 39.6217431765274,1.28924554427428 --trim3 3 --mp 9.52391186660738,5.98713335111101 --local --large-index -k 2 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1157s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1157s Warning: skipping read '6' because it was < 2 characters long 1157s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1157s Warning: skipping read '10' because it was < 2 characters long 1157s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1157s Warning: skipping read '20' because it was < 2 characters long 1157s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1157s Warning: skipping read '23' because it was < 2 characters long 1157s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1157s Warning: skipping read '38' because it was < 2 characters long 1157s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1157s Warning: skipping read '53' because it was < 2 characters long 1157s 53 reads; of these: 1157s 53 (100.00%) were unpaired; of these: 1157s 53 (100.00%) aligned 0 times 1157s 0 (0.00%) aligned exactly 1 time 1157s 0 (0.00%) aligned >1 times 1157s 0.00% overall alignment rate 1157s Read 50 alignments... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s --- Summary --- 1157s Read 1 reference strings 1157s Checked 0 alignments, 0 edits 1157s --------------- 1157s PASSED 1157s Flattened IUPAC characters 1157s Mutating sequence Sim.pm.2 1157s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1157s Finished SNPs 1157s Finished ref gaps 1157s Finished read gaps 1157s Mutating sequence Sim.pm.1 1157s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1157s Finished SNPs 1157s Finished ref gaps 1157s Finished read gaps 1157s Mutated reference genome to subject genome 1157s SNPs introduced: 4 1157s Reference gaps introduced: 0 1157s Read gaps introduced: 1 1157s Rearrangements introduced: 1 1157s Created read sampler 1157s Sampling 45 reads 1157s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1157s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1157s parsing sequence Sim.pm.1... 1157s parsing sequence Sim.pm.2... 1157s Parsed 269 reference bases 1157s *** Run 64 of 100 1157s /usr/bin/bowtie2 --trim3 3 --large-index --n-ceil 1.47428402458976,0.859143781255568 -M 3 --score-min L,1.59078822574439,6.20235026124854 --cp-min 3 -N 0 -L15 --cp-ival 4 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1157s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1157s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 1157s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1157s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 1157s Warning: skipping mate #2 of read '41' because it was < 2 characters long 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1157s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1157s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1157s 45 reads; of these: 1157s 42 (93.33%) were paired; of these: 1157s 42 (100.00%) aligned concordantly 0 times 1157s 0 (0.00%) aligned concordantly exactly 1 time 1157s 0 (0.00%) aligned concordantly >1 times 1157s ---- 1157s 42 pairs aligned concordantly 0 times; of these: 1157s 0 (0.00%) aligned discordantly 1 time 1157s ---- 1157s 42 pairs aligned 0 times concordantly or discordantly; of these: 1157s 84 mates make up the pairs; of these: 1157s 65 (77.38%) aligned 0 times 1157s 5 (5.95%) aligned exactly 1 time 1157s 14 (16.67%) aligned >1 times 1157s 3 (6.67%) were unpaired; of these: 1157s 2 (66.67%) aligned 0 times 1157s 0 (0.00%) aligned exactly 1 time 1157s 1 (33.33%) aligned >1 times 1157s 22.99% overall alignment rate 1157s Read 50 alignments... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s CTG 1157s CTG 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s AA 1157s AA 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s TATGGTGAGGGTCGAGGAC 1157s TATGGTGAGGGTCGAGGAC 1157s Processing line... 1157s GG 1157s GG 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s GTAGAACACGAGCCTGTCACATCGAGATGGACCACC 1157s GTAGAACACGAGCCTGTCACATCGAGATGGACCACC 1157s Processing line... 1157s Processing line... 1157s TA 1157s TA 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s TAGAACACGAGCCTGTCACATCGAGATGGA 1157s TAGAACACGAGCCTGTCACATCGAGATGGA 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s ACACGAGCCTGTCACATCGAGAT 1157s ACACGAGCCTGTCACATCGAGAT 1157s Processing line... 1157s Processing line... 1157s AG 1157s AG 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s ATTAGAGCTCGCAGC 1157s ATTAGAGCTCGCAGC 1157s Processing line... 1157s Processing line... 1157s CTGTCACATCGAGATGGACCACCTC 1157s CTGTCACATCGAGATGGACCACCTC 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s /usr/bin/bowtie2 --trim3 3 --large-index --n-ceil 1.47428402458976,0.859143781255568 -M 3 --score-min L,1.59078822574439,6.20235026124854 --cp-min 3 -N 0 -L15 --cp-ival 4 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s TCACATCGAGATGGACCACC 1157s TCACATCGAGATGGACCACC 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s TGTCACATCGAGATGGAC 1157s TGTCACATCGAGATGGAC 1157s Processing line... 1157s Processing line... 1157s AACACGAGCCTGTCA 1157s AACACGAGCCTGTCA 1157s Processing line... 1157s Processing line... 1157s GTG 1157s GTG 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s CCTC 1157s CCTC 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s ATAACCAAAACGC 1157s ATAACCAAAACGC 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s TATGG 1157s TATGG 1157s Processing line... 1157s Processing line... 1157s ACCTC 1157s ACCTC 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s TATG 1157s TATG 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s Processing line... 1157s --- Summary --- 1157s Read 1 reference strings 1157s Checked 20 alignments, 0 edits 1157s --------------- 1157s PASSED 1157s ALSO checking that bowtie2 and bowtie2-align match up 1157s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1157s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 1157s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1157s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 1157s Warning: skipping mate #2 of read '41' because it was < 2 characters long 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1157s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1157s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1157s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1157s 45 reads; of these: 1157s 42 (93.33%) were paired; of these: 1157s 42 (100.00%) aligned concordantly 0 times 1157s 0 (0.00%) aligned concordantly exactly 1 time 1157s 0 (0.00%) aligned concordantly >1 times 1157s ---- 1157s 42 pairs aligned concordantly 0 times; of these: 1157s 0 (0.00%) aligned discordantly 1 time 1157s ---- 1157s 42 pairs aligned 0 times concordantly or discordantly; of these: 1157s 84 mates make up the pairs; of these: 1157s 65 (77.38%) aligned 0 times 1157s 5 (5.95%) aligned exactly 1 time 1157s 14 (16.67%) aligned >1 times 1157s 3 (6.67%) were unpaired; of these: 1157s 2 (66.67%) aligned 0 times 1157s 0 (0.00%) aligned exactly 1 time 1157s 1 (33.33%) aligned >1 times 1157s 22.99% overall alignment rate 1157s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1157s /usr/bin/bowtie2 --trim3 3 --large-index --n-ceil 1.47428402458976,0.859143781255568 -M 3 --score-min L,1.59078822574439,6.20235026124854 --cp-min 3 -N 0 -L15 --cp-ival 4 -q -p 2 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1157s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1158s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1158s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 1158s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1158s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 1158s Warning: skipping mate #2 of read '41' because it was < 2 characters long 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1158s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1158s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1158s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1158s 45 reads; of these: 1158s 42 (93.33%) were paired; of these: 1158s 42 (100.00%) aligned concordantly 0 times 1158s 0 (0.00%) aligned concordantly exactly 1 time 1158s 0 (0.00%) aligned concordantly >1 times 1158s ---- 1158s 42 pairs aligned concordantly 0 times; of these: 1158s 0 (0.00%) aligned discordantly 1 time 1158s ---- 1158s 42 pairs aligned 0 times concordantly or discordantly; of these: 1158s 84 mates make up the pairs; of these: 1158s 65 (77.38%) aligned 0 times 1158s 5 (5.95%) aligned exactly 1 time 1158s 14 (16.67%) aligned >1 times 1158s 3 (6.67%) were unpaired; of these: 1158s 2 (66.67%) aligned 0 times 1158s 0 (0.00%) aligned exactly 1 time 1158s 1 (33.33%) aligned >1 times 1158s 22.99% overall alignment rate 1158s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1158s Flattened IUPAC characters 1158s Mutating sequence Sim.pm.2 1158s Introducing 13 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1158s Finished SNPs 1158s Finished ref gaps 1158s Finished read gaps 1158s Mutating sequence Sim.pm.1 1158s Introducing 5 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1158s Finished SNPs 1158s Finished ref gaps 1158s Finished read gaps 1158s Mutated reference genome to subject genome 1158s SNPs introduced: 18 1158s Reference gaps introduced: 1 1158s Read gaps introduced: 2 1158s Rearrangements introduced: 0 1158s Created read sampler 1158s Sampling 125 reads 1158s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1158s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1158s parsing sequence Sim.pm.1... 1158s parsing sequence Sim.pm.2... 1158s Parsed 269 reference bases 1158s *** Run 65 of 100 1158s /usr/bin/bowtie2 --local --rfg 26.5495477722546,11.6048221063846 --trim5 6 --rdg 15.1649080803698,6.87520234584445 --score-min L,7.94575668563569,7.40310417267674 --gbar 4 --large-index --cp-min 7 --cp-ival 1 --mm -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw 1158s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '1' because it was < 2 characters long 1158s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '7' because it was < 2 characters long 1158s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '11' because it was < 2 characters long 1158s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '23' because it was < 2 characters long 1158s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '24' because it was < 2 characters long 1158s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '28' because it was < 2 characters long 1158s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '49' because it was < 2 characters long 1158s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '51' because it was < 2 characters long 1158s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '66' because it was < 2 characters long 1158s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '67' because it was < 2 characters long 1158s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '72' because it was < 2 characters long 1158s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '92' because it was < 2 characters long 1158s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '94' because it was < 2 characters long 1158s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '105' because it was < 2 characters long 1158s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '111' because it was < 2 characters long 1158s Read 50 alignments... 1158s Warning: skipping read '113' because length (1) <= # seed mismatches (0) 1158s Read 100 alignments... 1158s Warning: skipping read '113' because it was < 2 characters long 1158s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '116' because it was < 2 characters long 1158s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '118' because it was < 2 characters long 1158s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '121' because it was < 2 characters long 1158s 125 reads; of these: 1158s 125 (100.00%) were unpaired; of these: 1158s 125 (100.00%) aligned 0 times 1158s 0 (0.00%) aligned exactly 1 time 1158s 0 (0.00%) aligned >1 times 1158s 0.00% overall alignment rate 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s /usr/bin/bowtie2 --local --rfg 26.5495477722546,11.6048221063846 --trim5 6 --rdg 15.1649080803698,6.87520234584445 --score-min L,7.94575668563569,7.40310417267674 --gbar 4 --large-index --cp-min 7 --cp-ival 1 --mm -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s Processing line... 1158s --- Summary --- 1158s Read 1 reference strings 1158s Checked 0 alignments, 0 edits 1158s --------------- 1158s PASSED 1158s ALSO checking that bowtie2 and bowtie2-align match up 1158s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '1' because it was < 2 characters long 1158s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '7' because it was < 2 characters long 1158s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '11' because it was < 2 characters long 1158s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '23' because it was < 2 characters long 1158s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '24' because it was < 2 characters long 1158s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '28' because it was < 2 characters long 1158s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '49' because it was < 2 characters long 1158s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '51' because it was < 2 characters long 1158s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '66' because it was < 2 characters long 1158s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '67' because it was < 2 characters long 1158s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '72' because it was < 2 characters long 1158s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '92' because it was < 2 characters long 1158s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '94' because it was < 2 characters long 1158s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '105' because it was < 2 characters long 1158s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '111' because it was < 2 characters long 1158s Warning: skipping read '113' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '113' because it was < 2 characters long 1158s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '116' because it was < 2 characters long 1158s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '118' because it was < 2 characters long 1158s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '121' because it was < 2 characters long 1158s 125 reads; of these: 1158s 125 (100.00%) were unpaired; of these: 1158s 125 (100.00%) aligned 0 times 1158s 0 (0.00%) aligned exactly 1 time 1158s 0 (0.00%) aligned >1 times 1158s 0.00% overall alignment rate 1158s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1158s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1158s /usr/bin/bowtie2 --local --rfg 26.5495477722546,11.6048221063846 --trim5 6 --rdg 15.1649080803698,6.87520234584445 --score-min L,7.94575668563569,7.40310417267674 --gbar 4 --large-index --cp-min 7 --cp-ival 1 --mm -r -p 4 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1158s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '1' because it was < 2 characters long 1158s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '7' because it was < 2 characters long 1158s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '11' because it was < 2 characters long 1158s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '23' because it was < 2 characters long 1158s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '24' because it was < 2 characters long 1158s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '28' because it was < 2 characters long 1158s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '49' because it was < 2 characters long 1158s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '51' because it was < 2 characters long 1158s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '92' because it was < 2 characters long 1158s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '94' because it was < 2 characters long 1158s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '66' because it was < 2 characters long 1158s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '67' because it was < 2 characters long 1158s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '72' because it was < 2 characters long 1158s Warning: skipping read '113' because length (1) <= # seed mismatches (0) 1158s Warning: skipping read '113' because it was < 2 characters long 1158s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '116' because it was < 2 characters long 1158s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '118' because it was < 2 characters long 1158s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '121' because it was < 2 characters long 1158s Warning: skipping read '105' because it was < 2 characters long 1158s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 1158s Warning: skipping read '111' because it was < 2 characters long 1158s 125 reads; of these: 1158s 125 (100.00%) were unpaired; of these: 1158s 125 (100.00%) aligned 0 times 1158s 0 (0.00%) aligned exactly 1 time 1158s 0 (0.00%) aligned >1 times 1158s 0.00% overall alignment rate 1158s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1158s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1158s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1158s Flattened IUPAC characters 1158s Mutating sequence Sim.pm.1 1158s Introducing 2 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1158s Finished SNPs 1158s Finished ref gaps 1158s Finished read gaps 1158s Mutating sequence Sim.pm.2 1158s Introducing 5 SNPs, 2/0 ref/read gaps, and 2 rearrangements 1158s Finished SNPs 1158s Finished ref gaps 1158s Finished read gaps 1158s Mutated reference genome to subject genome 1158s SNPs introduced: 7 1158s Reference gaps introduced: 2 1158s Read gaps introduced: 0 1158s Rearrangements introduced: 4 1158s Created read sampler 1158s Sampling 132 reads 1158s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1158s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1158s parsing sequence Sim.pm.1... 1158s parsing sequence Sim.pm.2... 1158s Parsed 269 reference bases 1158s *** Run 66 of 100 1158s /usr/bin/bowtie2 -k 8 --large-index --local --trim3 8 --rdg 11.7609085215615,18.7545092795665 --cp-ival 2 --mm --cp-min 7 --score-min L,8.24978230252466,9.7103549760674 --np 1 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq 1159s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1159s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 1159s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1159s Read 50 alignments... 1159s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1159s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 1159s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 1159s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 1159s Read 100 alignments... 1159s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 1159s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 1159s Read 150 alignments... 1159s 132 reads; of these: 1159s 107 (81.06%) were paired; of these: 1159s 107 (100.00%) aligned concordantly 0 times 1159s 0 (0.00%) aligned concordantly exactly 1 time 1159s 0 (0.00%) aligned concordantly >1 times 1159s ---- 1159s 107 pairs aligned concordantly 0 times; of these: 1159s 0 (0.00%) aligned discordantly 1 time 1159s ---- 1159s 107 pairs aligned 0 times concordantly or discordantly; of these: 1159s 214 mates make up the pairs; of these: 1159s 214 (100.00%) aligned 0 times 1159s 0 (0.00%) aligned exactly 1 time 1159s 0 (0.00%) aligned >1 times 1159s 25 (18.94%) were unpaired; of these: 1159s 25 (100.00%) aligned 0 times 1159s 0 (0.00%) aligned exactly 1 time 1159s 0 (0.00%) aligned >1 times 1159s 0.00% overall alignment rate 1159s Read 200 alignments... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s 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Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s Processing line... 1159s --- Summary --- 1159s Read 1 reference strings 1159s Checked 0 alignments, 0 edits 1159s --------------- 1159s PASSED 1159s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1159s /usr/bin/bowtie2 -k 8 --large-index --local --trim3 8 --rdg 11.7609085215615,18.7545092795665 --cp-ival 2 --mm --cp-min 7 --score-min L,8.24978230252466,9.7103549760674 --np 1 --qseq -p 3 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1159s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 1159s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 1159s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 1159s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 1159s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1159s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 1159s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1159s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 1159s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 1159s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 1159s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 1159s 132 reads; of these: 1159s 107 (81.06%) were paired; of these: 1159s 107 (100.00%) aligned concordantly 0 times 1159s 0 (0.00%) aligned concordantly exactly 1 time 1159s 0 (0.00%) aligned concordantly >1 times 1159s ---- 1159s 107 pairs aligned concordantly 0 times; of these: 1159s 0 (0.00%) aligned discordantly 1 time 1159s ---- 1159s 107 pairs aligned 0 times concordantly or discordantly; of these: 1159s 214 mates make up the pairs; of these: 1159s 214 (100.00%) aligned 0 times 1159s 0 (0.00%) aligned exactly 1 time 1159s 0 (0.00%) aligned >1 times 1159s 25 (18.94%) were unpaired; of these: 1159s 25 (100.00%) aligned 0 times 1159s 0 (0.00%) aligned exactly 1 time 1159s 0 (0.00%) aligned >1 times 1159s 0.00% overall alignment rate 1159s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1159s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1159s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1159s Flattened IUPAC characters 1159s Mutating sequence Sim.pm.1 1159s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1159s Finished SNPs 1159s Finished ref gaps 1159s Finished read gaps 1159s Mutating sequence Sim.pm.2 1159s Introducing 4 SNPs, 3/0 ref/read gaps, and 3 rearrangements 1159s Finished SNPs 1159s Finished ref gaps 1159s Finished read gaps 1159s Mutated reference genome to subject genome 1159s SNPs introduced: 4 1159s Reference gaps introduced: 4 1159s Read gaps introduced: 0 1159s Rearrangements introduced: 3 1159s Created read sampler 1159s Sampling 107 reads 1159s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1159s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1159s parsing sequence Sim.pm.1... 1159s parsing sequence Sim.pm.2... 1159s Parsed 269 reference bases 1159s *** Run 67 of 100 1159s /usr/bin/bowtie2 --cp-min 5 --cp-ival 2 --trim3 4 --large-index -M 2 -D 45 --rfg 21.436905226734 -i C,0.54802308631221 --gbar 6 --score-min L,3.30113593237314,4.52103791678707 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1159s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1159s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 1159s Warning: skipping read '15' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1159s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read '17' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1159s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 1159s Warning: skipping read '23' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1159s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read '26' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1159s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read '36' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1159s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read '48' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1159s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 1159s Warning: skipping read '49' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1159s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read '50' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1159s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 1159s Warning: skipping read '51' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1159s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read '53' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1159s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1159s Warning: skipping read '57' because it was < 2 characters long 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1159s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1160s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '84' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1160s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 1160s Warning: skipping read '86' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1160s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '91' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1160s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '101' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1160s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '107' because it was < 2 characters long 1160s 107 reads; of these: 1160s 107 (100.00%) were unpaired; of these: 1160s 87 (81.31%) aligned 0 times 1160s 8 (7.48%) aligned exactly 1 time 1160s 12 (11.21%) aligned >1 times 1160s 18.69% overall alignment rate 1160s Read 50 alignments... 1160s Read 100 alignments... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s ACACGAGCCTGTCACATCGAGATGGA 1160s ACACGAGCCTGTCACATCGAGATGGA 1160s Processing line... 1160s GGTAT 1160s GGTAT 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s ACCTC 1160s ACCTC 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s GCTGAAG 1160s GCTGAAG 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s AACACG 1160s AACACG 1160s Processing line... 1160s Processing line... 1160s GCC 1160s GCC 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s CCACCTCG 1160s CCACCTCG 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s ATG 1160s ATG 1160s Processing line... 1160s TGG 1160s TGG 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s GCTGAAGTGGCTGAGA 1160s GCTGAAGTGGCTGAGA 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s GAGAC 1160s GAGAC 1160s Processing line... 1160s CAGCG 1160s CAGCG 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s CGTA 1160s CGTA 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s CTGTCACATCGAGATGGAC 1160s CTGTCACATCGAGATGGAC 1160s Processing line... 1160s Processing line... 1160s GCTGAAG 1160s GCTGAAG 1160s Processing line... 1160s AACACGAGCCTGTC 1160s AACACGAGCCTGTC 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s GAAC 1160s GAAC 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s GAAATTA 1160s GAAATTA 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s AG 1160s AG 1160s Processing line... 1160s Processing line... 1160s Processing line... 1160s TAGAACAC 1160s TAGAACAC 1160s Processing line... 1160s Processing line... 1160s --- Summary --- 1160s Read 1 reference strings 1160s Checked 20 alignments, 0 edits 1160s --------------- 1160s PASSED 1160s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1160s /usr/bin/bowtie2 --cp-min 5 --cp-ival 2 --trim3 4 --large-index -M 2 -D 45 --rfg 21.436905226734 -i C,0.54802308631221 --gbar 6 --score-min L,3.30113593237314,4.52103791678707 -q -p 4 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1160s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1160s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '17' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1160s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 1160s Warning: skipping read '49' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1160s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '50' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1160s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 1160s Warning: skipping read '51' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1160s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '53' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1160s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 1160s Warning: skipping read '23' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1160s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '26' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1160s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '36' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1160s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 1160s Warning: skipping read '15' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1160s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '57' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1160s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '84' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1160s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 1160s Warning: skipping read '86' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1160s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '91' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1160s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '101' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1160s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '107' because it was < 2 characters long 1160s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1160s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 1160s Warning: skipping read '48' because it was < 2 characters long 1161s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1161s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1161s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1161s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1162s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1162s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1162s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1162s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1162s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1162s 107 reads; of these: 1162s 107 (100.00%) were unpaired; of these: 1162s 87 (81.31%) aligned 0 times 1162s 8 (7.48%) aligned exactly 1 time 1162s 12 (11.21%) aligned >1 times 1162s 18.69% overall alignment rate 1162s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1162s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1162s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1162s Flattened IUPAC characters 1162s Mutating sequence Sim.pm.2 1162s Introducing 23 SNPs, 0/2 ref/read gaps, and 1 rearrangements 1162s Finished SNPs 1162s Finished ref gaps 1162s Finished read gaps 1162s Mutating sequence Sim.pm.1 1162s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1162s Finished SNPs 1162s Finished ref gaps 1162s Finished read gaps 1162s Mutated reference genome to subject genome 1162s SNPs introduced: 24 1162s Reference gaps introduced: 0 1162s Read gaps introduced: 2 1162s Rearrangements introduced: 1 1162s Created read sampler 1162s Sampling 70 reads 1162s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1162s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1162s parsing sequence Sim.pm.1... 1162s parsing sequence Sim.pm.2... 1162s Parsed 269 reference bases 1162s *** Run 68 of 100 1162s /usr/bin/bowtie2 --nofw --norc -D 30 -R 1 -N 1 -L17 --score-min L,4.37998606697601,3.27542977426738 --gbar 6 --n-ceil 0.257412069654104,1.09410736500245 --cp-min 2 --cp-ival 2 --local --mp 7.45157845988133,4.81930792361553 -a --trim3 2 --large-index -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1163s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '34' because it was < 2 characters long 1163s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '42' because it was < 2 characters long 1163s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '45' because it was < 2 characters long 1163s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '51' because it was < 2 characters long 1163s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '52' because it was < 2 characters long 1163s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '54' because it was < 2 characters long 1163s 70 reads; of these: 1163s 70 (100.00%) were unpaired; of these: 1163s 70 (100.00%) aligned 0 times 1163s 0 (0.00%) aligned exactly 1 time 1163s 0 (0.00%) aligned >1 times 1163s 0.00% overall alignment rate 1163s Read 50 alignments... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s /usr/bin/bowtie2 --nofw --norc -D 30 -R 1 -N 1 -L17 --score-min L,4.37998606697601,3.27542977426738 --gbar 6 --n-ceil 0.257412069654104,1.09410736500245 --cp-min 2 --cp-ival 2 --local --mp 7.45157845988133,4.81930792361553 -a --trim3 2 --large-index -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s Processing line... 1163s --- Summary --- 1163s Read 1 reference strings 1163s Checked 0 alignments, 0 edits 1163s --------------- 1163s PASSED 1163s ALSO checking that bowtie2 and bowtie2-align match up 1163s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '34' because it was < 2 characters long 1163s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '42' because it was < 2 characters long 1163s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '45' because it was < 2 characters long 1163s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '51' because it was < 2 characters long 1163s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '52' because it was < 2 characters long 1163s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '54' because it was < 2 characters long 1163s 70 reads; of these: 1163s 70 (100.00%) were unpaired; of these: 1163s 70 (100.00%) aligned 0 times 1163s 0 (0.00%) aligned exactly 1 time 1163s 0 (0.00%) aligned >1 times 1163s 0.00% overall alignment rate 1163s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1163s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1163s /usr/bin/bowtie2 --nofw --norc -D 30 -R 1 -N 1 -L17 --score-min L,4.37998606697601,3.27542977426738 --gbar 6 --n-ceil 0.257412069654104,1.09410736500245 --cp-min 2 --cp-ival 2 --local --mp 7.45157845988133,4.81930792361553 -a --trim3 2 --large-index -q -p 2 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1163s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '34' because it was < 2 characters long 1163s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '51' because it was < 2 characters long 1163s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '52' because it was < 2 characters long 1163s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '54' because it was < 2 characters long 1163s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '42' because it was < 2 characters long 1163s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 1163s Warning: skipping read '45' because it was < 2 characters long 1163s 70 reads; of these: 1163s 70 (100.00%) were unpaired; of these: 1163s 70 (100.00%) aligned 0 times 1163s 0 (0.00%) aligned exactly 1 time 1163s 0 (0.00%) aligned >1 times 1163s 0.00% overall alignment rate 1163s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1163s Flattened IUPAC characters 1163s Mutating sequence Sim.pm.1 1163s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1163s Finished SNPs 1163s Finished ref gaps 1163s Finished read gaps 1163s Mutating sequence Sim.pm.2 1163s Introducing 20 SNPs, 5/0 ref/read gaps, and 0 rearrangements 1163s Finished SNPs 1163s Finished ref gaps 1163s Finished read gaps 1163s Mutated reference genome to subject genome 1163s SNPs introduced: 24 1163s Reference gaps introduced: 5 1163s Read gaps introduced: 0 1163s Rearrangements introduced: 0 1163s Created read sampler 1163s Sampling 80 reads 1163s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1163s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1163s parsing sequence Sim.pm.1... 1163s *** Run 69 of 100 1163s /usr/bin/bowtie2 --local --rdg 19.6597287753024,5.81866653663416 --trim3 0 --large-index --cp-min 3 --cp-ival 1 --rfg 4.04789182593618,9.98805654700138 --trim5 6 --score-min L,5.59611344554911,3.29970619337402 --norc -D 37 --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1163s parsing sequence Sim.pm.2... 1163s Parsed 269 reference bases 1164s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1164s 80 reads; of these: 1164s 80 (100.00%) were unpaired; of these: 1164s 80 (100.00%) aligned 0 times 1164s 0 (0.00%) aligned exactly 1 time 1164s 0 (0.00%) aligned >1 times 1164s 0.00% overall alignment rate 1164s Read 50 alignments... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s --- Summary --- 1164s Read 1 reference strings 1164s Checked 0 alignments, 0 edits 1164s --------------- 1164s PASSED 1164s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1164s /usr/bin/bowtie2 --local --rdg 19.6597287753024,5.81866653663416 --trim3 0 --large-index --cp-min 3 --cp-ival 1 --rfg 4.04789182593618,9.98805654700138 --trim5 6 --score-min L,5.59611344554911,3.29970619337402 --norc -D 37 --qseq -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1164s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 1164s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 1164s 80 reads; of these: 1164s 80 (100.00%) were unpaired; of these: 1164s 80 (100.00%) aligned 0 times 1164s 0 (0.00%) aligned exactly 1 time 1164s 0 (0.00%) aligned >1 times 1164s 0.00% overall alignment rate 1164s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1164s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1164s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1164s Flattened IUPAC characters 1164s Mutating sequence Sim.pm.2 1164s Introducing 5 SNPs, 3/0 ref/read gaps, and 0 rearrangements 1164s Finished SNPs 1164s Finished ref gaps 1164s Finished read gaps 1164s Mutating sequence Sim.pm.1 1164s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1164s Finished SNPs 1164s Finished ref gaps 1164s Finished read gaps 1164s Mutated reference genome to subject genome 1164s SNPs introduced: 6 1164s Reference gaps introduced: 3 1164s Read gaps introduced: 0 1164s Rearrangements introduced: 0 1164s Created read sampler 1164s Sampling 63 reads 1164s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1164s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1164s parsing sequence Sim.pm.1... 1164s parsing sequence Sim.pm.2... 1164s Parsed 269 reference bases 1164s *** Run 70 of 100 1164s /usr/bin/bowtie2 --mp 8.25817567666291,3.88922256165367 --trim3 4 --trim5 4 --local --large-index --score-min L,8.20170826797616,8.12252271986307 --cp-min 5 --cp-ival 1 -D 31 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1164s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1164s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1164s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read '25' because it was < 2 characters long 1164s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1164s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1164s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 1164s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1164s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 1164s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1164s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1164s Warning: skipping read '35' because it was < 2 characters long 1164s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1164s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1164s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 1164s Warning: skipping mate #2 of read '48' because it was < 2 characters long 1164s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 1164s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1164s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1164s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1164s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 1164s Warning: skipping mate #1 of read '58' because it was < 2 characters long 1164s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 1164s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1164s 63 reads; of these: 1164s 52 (82.54%) were paired; of these: 1164s 52 (100.00%) aligned concordantly 0 times 1164s 0 (0.00%) aligned concordantly exactly 1 time 1164s 0 (0.00%) aligned concordantly >1 times 1164s ---- 1164s 52 pairs aligned concordantly 0 times; of these: 1164s 0 (0.00%) aligned discordantly 1 time 1164s ---- 1164s 52 pairs aligned 0 times concordantly or discordantly; of these: 1164s 104 mates make up the pairs; of these: 1164s 104 (100.00%) aligned 0 times 1164s 0 (0.00%) aligned exactly 1 time 1164s 0 (0.00%) aligned >1 times 1164s 11 (17.46%) were unpaired; of these: 1164s 11 (100.00%) aligned 0 times 1164s 0 (0.00%) aligned exactly 1 time 1164s 0 (0.00%) aligned >1 times 1164s 0.00% overall alignment rate 1164s Read 50 alignments... 1164s Read 100 alignments... 1164s /usr/bin/bowtie2 --mp 8.25817567666291,3.88922256165367 --trim3 4 --trim5 4 --local --large-index --score-min L,8.20170826797616,8.12252271986307 --cp-min 5 --cp-ival 1 -D 31 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s Processing line... 1164s --- Summary --- 1164s Read 1 reference strings 1164s Checked 0 alignments, 0 edits 1164s --------------- 1164s PASSED 1164s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1165s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1165s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1165s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '25' because it was < 2 characters long 1165s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 1165s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1165s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 1165s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1165s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 1165s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1165s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '35' because it was < 2 characters long 1165s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1165s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1165s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 1165s Warning: skipping mate #2 of read '48' because it was < 2 characters long 1165s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 1165s Warning: skipping mate #1 of read '51' because it was < 2 characters long 1165s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 1165s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1165s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 1165s Warning: skipping mate #1 of read '58' because it was < 2 characters long 1165s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 1165s Warning: skipping mate #1 of read '59' because it was < 2 characters long 1165s 63 reads; of these: 1165s 52 (82.54%) were paired; of these: 1165s 52 (100.00%) aligned concordantly 0 times 1165s 0 (0.00%) aligned concordantly exactly 1 time 1165s 0 (0.00%) aligned concordantly >1 times 1165s ---- 1165s 52 pairs aligned concordantly 0 times; of these: 1165s 0 (0.00%) aligned discordantly 1 time 1165s ---- 1165s 52 pairs aligned 0 times concordantly or discordantly; of these: 1165s 104 mates make up the pairs; of these: 1165s 104 (100.00%) aligned 0 times 1165s 0 (0.00%) aligned exactly 1 time 1165s 0 (0.00%) aligned >1 times 1165s 11 (17.46%) were unpaired; of these: 1165s 11 (100.00%) aligned 0 times 1165s 0 (0.00%) aligned exactly 1 time 1165s 0 (0.00%) aligned >1 times 1165s 0.00% overall alignment rate 1165s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1165s Flattened IUPAC characters 1165s Mutating sequence Sim.pm.1 1165s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1165s Finished SNPs 1165s Finished ref gaps 1165s Finished read gaps 1165s Mutating sequence Sim.pm.2 1165s Introducing 26 SNPs, 5/3 ref/read gaps, and 1 rearrangements 1165s Finished SNPs 1165s Finished ref gaps 1165s Finished read gaps 1165s Mutated reference genome to subject genome 1165s SNPs introduced: 33 1165s Reference gaps introduced: 5 1165s Read gaps introduced: 4 1165s Rearrangements introduced: 1 1165s Created read sampler 1165s Sampling 143 reads 1165s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1165s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1165s parsing sequence Sim.pm.1... 1165s parsing sequence Sim.pm.2... 1165s Parsed 269 reference bases 1165s *** Run 71 of 100 1165s /usr/bin/bowtie2 --trim5 5 -i S,2.72764147019457 --rfg 43.2135507795735 --gbar 3 --score-min L,6.3598439649617,1.74764818630651 --np 2 -D 18 --rdg 47.388250210323 --local --large-index --cp-min 10 --mm --cp-ival 1 -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw 1165s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '1' because it was < 2 characters long 1165s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '9' because it was < 2 characters long 1165s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1165s Warning: skipping read '10' because it was < 2 characters long 1165s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '15' because it was < 2 characters long 1165s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '24' because it was < 2 characters long 1165s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '30' because it was < 2 characters long 1165s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '37' because it was < 2 characters long 1165s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '45' because it was < 2 characters long 1165s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '47' because it was < 2 characters long 1165s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '56' because it was < 2 characters long 1165s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '60' because it was < 2 characters long 1165s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '65' because it was < 2 characters long 1165s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '67' because it was < 2 characters long 1165s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '72' because it was < 2 characters long 1165s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '73' because it was < 2 characters long 1165s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '84' because it was < 2 characters long 1165s Warning: skipping read '85' because length (1) <= # seed mismatches (0) 1165s Warning: skipping read '85' because it was < 2 characters long 1165s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '87' because it was < 2 characters long 1165s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 1165s Warning: skipping read '95' because it was < 2 characters long 1165s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '97' because it was < 2 characters long 1165s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '113' because it was < 2 characters long 1165s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '118' because it was < 2 characters long 1165s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '123' because it was < 2 characters long 1165s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '125' because it was < 2 characters long 1165s Warning: skipping read '126' because length (1) <= # seed mismatches (0) 1165s Warning: skipping read '126' because it was < 2 characters long 1165s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '135' because it was < 2 characters long 1165s 143 reads; of these: 1165s 143 (100.00%) were unpaired; of these: 1165s 141 (98.60%) aligned 0 times 1165s 0 (0.00%) aligned exactly 1 time 1165s 2 (1.40%) aligned >1 times 1165s 1.40% overall alignment rate 1165s Read 50 alignments... 1165s Read 100 alignments... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGATGGATAACCAAAGTAGAA 1165s AGTAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGGNTGGATAACCANAGTAGAA 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s AGAACACGAGCCTGTCACATCGAGATGGACCAC 1165s AGAACACGAGCCTGTCACATCGAGATGGACCAC 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s Processing line... 1165s --- Summary --- 1165s Read 1 reference strings 1165s Checked 2 alignments, 0 edits 1165s --------------- 1165s PASSED 1165s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1165s /usr/bin/bowtie2 --trim5 5 -i S,2.72764147019457 --rfg 43.2135507795735 --gbar 3 --score-min L,6.3598439649617,1.74764818630651 --np 2 -D 18 --rdg 47.388250210323 --local --large-index --cp-min 10 --mm --cp-ival 1 -r -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1165s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '1' because it was < 2 characters long 1165s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '9' because it was < 2 characters long 1165s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1165s Warning: skipping read '10' because it was < 2 characters long 1165s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '15' because it was < 2 characters long 1165s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '37' because it was < 2 characters long 1165s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '45' because it was < 2 characters long 1165s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '47' because it was < 2 characters long 1165s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '65' because it was < 2 characters long 1165s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '67' because it was < 2 characters long 1165s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '72' because it was < 2 characters long 1165s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '73' because it was < 2 characters long 1165s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '24' because it was < 2 characters long 1165s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '30' because it was < 2 characters long 1165s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '113' because it was < 2 characters long 1165s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '97' because it was < 2 characters long 1165s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '135' because it was < 2 characters long 1165s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '118' because it was < 2 characters long 1165s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '123' because it was < 2 characters long 1165s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '125' because it was < 2 characters long 1165s Warning: skipping read '126' because length (1) <= # seed mismatches (0) 1165s Warning: skipping read '126' because it was < 2 characters long 1165s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '84' because it was < 2 characters long 1165s Warning: skipping read '85' because length (1) <= # seed mismatches (0) 1165s Warning: skipping read '85' because it was < 2 characters long 1165s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '87' because it was < 2 characters long 1165s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 1165s Warning: skipping read '95' because it was < 2 characters long 1165s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '56' because it was < 2 characters long 1165s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 1165s Warning: skipping read '60' because it was < 2 characters long 1165s 143 reads; of these: 1165s 143 (100.00%) were unpaired; of these: 1165s 141 (98.60%) aligned 0 times 1165s 0 (0.00%) aligned exactly 1 time 1165s 2 (1.40%) aligned >1 times 1165s 1.40% overall alignment rate 1165s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1165s Flattened IUPAC characters 1165s Mutating sequence Sim.pm.2 1165s Introducing 18 SNPs, 1/1 ref/read gaps, and 2 rearrangements 1165s Finished SNPs 1165s Finished ref gaps 1165s Finished read gaps 1165s Mutating sequence Sim.pm.1 1165s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1165s Finished SNPs 1165s Finished ref gaps 1165s Finished read gaps 1165s Mutated reference genome to subject genome 1165s SNPs introduced: 26 1165s Reference gaps introduced: 1 1165s Read gaps introduced: 1 1165s Rearrangements introduced: 2 1165s Created read sampler 1165s Sampling 108 reads 1165s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1165s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1165s parsing sequence Sim.pm.1... 1165s *** Run 72 of 100 1165s /usr/bin/bowtie2 --rdg 27.1479577848578,11.850154027931 --score-min L,6.4970637174558,8.0295903261356 -k 2 --large-index --np 1 --cp-min 3 --cp-ival 2 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1165s parsing sequence Sim.pm.2... 1165s Parsed 269 reference bases 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1165s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1166s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 1166s Warning: skipping read '37' because it was < 2 characters long 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1166s Read 50 alignments... 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1166s Read 100 alignments... 1166s 108 reads; of these: 1166s 108 (100.00%) were unpaired; of these: 1166s 87 (80.56%) aligned 0 times 1166s 0 (0.00%) aligned exactly 1 time 1166s 21 (19.44%) aligned >1 times 1166s 19.44% overall alignment rate 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s TAA 1166s TAA 1166s Processing line... 1166s TAA 1166s TAA 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s GAGATGGA 1166s GAGATGGA 1166s Processing line... 1166s GAGATGGA 1166s GAGATGGA 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s GTCACATCGAGA 1166s GTCACATCGAGA 1166s Processing line... 1166s GTCACATCGAGA 1166s GTCACATCGAGA 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s GC 1166s GC 1166s Processing line... 1166s GC 1166s GC 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s CTCGTGGG 1166s CTCGTGGG 1166s Processing line... 1166s CTCGTGGG 1166s CTCGTGGG 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s CA 1166s CA 1166s Processing line... 1166s CA 1166s CA 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s GAGATGGACCA 1166s GAGATGGACCA 1166s Processing line... 1166s GAGATGGACCA 1166s GAGATGGACCA 1166s Processing line... 1166s Processing line... 1166s ATGGACC 1166s ATGGACC 1166s Processing line... 1166s ATGGACC 1166s ATGGACC 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s CCTGTCACATCGAGATGGACC 1166s CCTGTCACATCGAGATGGACC 1166s Processing line... 1166s CCTGTCACATCGAGATGGACC 1166s CCTGTCACATCGAGATGGACC 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s GT 1166s GT 1166s Processing line... 1166s GT 1166s GT 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s CGAGATGGACCAC 1166s CGAGATGGACCAC 1166s Processing line... 1166s CGAGATGGACCAC 1166s CGAGATGGACCAC 1166s Processing line... 1166s Processing line... 1166s AG 1166s AG 1166s Processing line... 1166s AG 1166s AG 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s CGAGCCTGTCACATC 1166s CGAGCCTGTCACATC 1166s Processing line... 1166s CGAGCCTGTCACATC 1166s CGAGCCTGTCACATC 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s TGG 1166s TGG 1166s Processing line... 1166s TGG 1166s TGG 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s ACGAGC 1166s ACGAGC 1166s Processing line... 1166s ACGAGC 1166s ACGAGC 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s CGAGATGGACCACCTCG 1166s CGAGATGGACCACCTCG 1166s Processing line... 1166s CGAGATGGACCACCTCG 1166s CGAGATGGACCACCTCG 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s GGATA 1166s GGATA 1166s Processing line... 1166s GGATA 1166s GGATA 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s TAG 1166s TAG 1166s Processing line... 1166s TAG 1166s TAG 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s ATAACC 1166s ATAACC 1166s Processing line... 1166s ATAACC 1166s ATAACC 1166s Processing line... 1166s ACACGAGCCT 1166s ACACGAGCCT 1166s Processing line... 1166s ACACGAGCCT 1166s ACACGAGCCT 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s TAGA 1166s TAGA 1166s Processing line... 1166s TAGA 1166s TAGA 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s Processing line... 1166s --- Summary --- 1166s Read 1 reference strings 1166s Checked 42 alignments, 0 edits 1166s --------------- 1166s PASSED 1166s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1166s /usr/bin/bowtie2 --rdg 27.1479577848578,11.850154027931 --score-min L,6.4970637174558,8.0295903261356 -k 2 --large-index --np 1 --cp-min 3 --cp-ival 2 -f -p 4 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1166s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 1166s Warning: skipping read '37' because it was < 2 characters long 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1166s 108 reads; of these: 1166s 108 (100.00%) were unpaired; of these: 1166s 87 (80.56%) aligned 0 times 1166s 0 (0.00%) aligned exactly 1 time 1166s 21 (19.44%) aligned >1 times 1166s 19.44% overall alignment rate 1166s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1166s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1166s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1166s /usr/bin/bowtie2 --rdg 27.1479577848578,11.850154027931 --score-min L,6.4970637174558,8.0295903261356 -k 2 --large-index --np 1 --cp-min 3 --cp-ival 2 -f -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1166s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1166s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 1166s Warning: skipping read '37' because it was < 2 characters long 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1166s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1166s 108 reads; of these: 1166s 108 (100.00%) were unpaired; of these: 1166s 87 (80.56%) aligned 0 times 1166s 0 (0.00%) aligned exactly 1 time 1166s 21 (19.44%) aligned >1 times 1166s 19.44% overall alignment rate 1166s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1166s Flattened IUPAC characters 1166s Mutating sequence Sim.pm.2 1166s Introducing 20 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1166s Finished SNPs 1166s Finished ref gaps 1166s Finished read gaps 1166s Mutating sequence Sim.pm.1 1166s Introducing 0 SNPs, 0/2 ref/read gaps, and 0 rearrangements 1166s Finished SNPs 1166s Finished ref gaps 1166s Finished read gaps 1166s Mutated reference genome to subject genome 1166s SNPs introduced: 20 1166s Reference gaps introduced: 1 1166s Read gaps introduced: 2 1166s Rearrangements introduced: 0 1166s Created read sampler 1166s Sampling 77 reads 1166s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1166s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1166s parsing sequence Sim.pm.1... 1166s parsing sequence Sim.pm.2... 1166s Parsed 269 reference bases 1166s *** Run 73 of 100 1166s /usr/bin/bowtie2 --cp-min 4 --cp-ival 1 --trim3 6 --mp 9.45689074873725,2.30676564950267 --score-min L,4.61628569401069,5.84864199260928 -k 4 --large-index -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1167s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 1167s Warning: skipping read '1' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1167s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '4' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1167s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '6' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1167s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '11' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1167s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '13' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1167s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 1167s Warning: skipping read '16' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1167s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 1167s Warning: skipping read '22' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1167s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '33' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1167s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '34' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1167s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '38' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1167s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '54' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1167s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '58' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1167s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '73' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1167s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '76' because it was < 2 characters long 1167s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1167s 77 reads; of these: 1167s 77 (100.00%) were unpaired; of these: 1167s 60 (77.92%) aligned 0 times 1167s 8 (10.39%) aligned exactly 1 time 1167s 9 (11.69%) aligned >1 times 1167s 22.08% overall alignment rate 1167s Read 50 alignments... 1167s Read 100 alignments... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s TCGAGAT 1167s TCGAGAT 1167s Processing line... 1167s TCGAGAT 1167s TCGAGAT 1167s Processing line... 1167s TCGAGAT 1167s TCGAGAT 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s GCTGAA 1167s GCTGAA 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s GAGC 1167s GAGC 1167s Processing line... 1167s GAGC 1167s GAGC 1167s Processing line... 1167s GAGC 1167s GAGC 1167s Processing line... 1167s GAGC 1167s GAGC 1167s Processing line... 1167s GAC 1167s GAC 1167s Processing line... 1167s GAC 1167s GAC 1167s Processing line... 1167s GAC 1167s GAC 1167s Processing line... 1167s GAC 1167s GAC 1167s Processing line... 1167s ATAACCAAAAC 1167s ATAACCAAAAC 1167s Processing line... 1167s TGGACCACCTCGTG 1167s TGGACCACCTCGTG 1167s Processing line... 1167s TGGACCACCTCGTG 1167s TGGACCACCTCGTG 1167s Processing line... 1167s TGGACCACCTCGTG 1167s TGGACCACCTCGTG 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s CACCTCGTGG 1167s CACCTCGTGG 1167s Processing line... 1167s CACCTCGTGG 1167s CACCTCGTGG 1167s Processing line... 1167s CACCTCGTGG 1167s CACCTCGTGG 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s TGGACC 1167s TGGACC 1167s Processing line... 1167s TGGACC 1167s TGGACC 1167s Processing line... 1167s TGGACC 1167s TGGACC 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s CCTGTCA 1167s CCTGTCA 1167s Processing line... 1167s CCTGTCA 1167s CCTGTCA 1167s Processing line... 1167s CCTGTCA 1167s CCTGTCA 1167s Processing line... 1167s Processing line... 1167s AAAC 1167s AAAC 1167s Processing line... 1167s AATTAGAGCT 1167s AATTAGAGCT 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s TGAAGTGG 1167s TGAAGTGG 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s CACATC 1167s CACATC 1167s Processing line... 1167s CACATC 1167s CACATC 1167s Processing line... 1167s CACATC 1167s CACATC 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s CGAGCCTGTCACATCGAGATGGA 1167s CGAGCCTGTCACATCGAGATGGA 1167s Processing line... 1167s CGAGCCTGTCACATCGAGATGGA 1167s CGAGCCTGTCACATCGAGATGGA 1167s Processing line... 1167s CGAGCCTGTCACATCGAGATGGA 1167s CGAGCCTGTCACATCGAGATGGA 1167s Processing line... 1167s Processing line... 1167s AGAGCT 1167s AGAGCT 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s CCAAA 1167s CCAAA 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s GATAACCAAA 1167s GATAACCAAA 1167s Processing line... 1167s Processing line... 1167s --- Summary --- 1167s Read 1 reference strings 1167s Checked 37 alignments, 0 edits 1167s --------------- 1167s PASSED 1167s Flattened IUPAC characters 1167s Mutating sequence Sim.pm.2 1167s Introducing 25 SNPs, 1/1 ref/read gaps, and 1 rearrangements 1167s Finished SNPs 1167s Finished ref gaps 1167s Finished read gaps 1167s Mutating sequence Sim.pm.1 1167s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1167s Finished SNPs 1167s Finished ref gaps 1167s Finished read gaps 1167s Mutated reference genome to subject genome 1167s SNPs introduced: 32 1167s Reference gaps introduced: 1 1167s Read gaps introduced: 1 1167s Rearrangements introduced: 1 1167s Created read sampler 1167s Sampling 21 reads 1167s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1167s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1167s parsing sequence Sim.pm.1... 1167s parsing sequence Sim.pm.2... 1167s Parsed 269 reference bases 1167s *** Run 74 of 100 1167s /usr/bin/bowtie2 --rfg 2.34518841483678,11.3435661518961 --trim5 6 --score-min L,5.16043077671743,2.33679265790962 --n-ceil 0.666492100177253,0.0847337326045927 --nofw --np 1 -D 31 -R 1 --local --mp 8.94535667698613,3.75120142793847 -a --trim3 0 --large-index --cp-min 2 --cp-ival 1 --mm -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw 1167s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '2' because it was < 2 characters long 1167s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '4' because it was < 2 characters long 1167s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '8' because it was < 2 characters long 1167s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '9' because it was < 2 characters long 1167s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '17' because it was < 2 characters long 1167s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 1167s Warning: skipping read '20' because it was < 2 characters long 1167s 21 reads; of these: 1167s 21 (100.00%) were unpaired; of these: 1167s 21 (100.00%) aligned 0 times 1167s 0 (0.00%) aligned exactly 1 time 1167s 0 (0.00%) aligned >1 times 1167s 0.00% overall alignment rate 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s --- Summary --- 1167s Read 1 reference strings 1167s Checked 0 alignments, 0 edits 1167s --------------- 1167s PASSED 1167s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1167s /usr/bin/bowtie2 --rfg 2.34518841483678,11.3435661518961 --trim5 6 --score-min L,5.16043077671743,2.33679265790962 --n-ceil 0.666492100177253,0.0847337326045927 --nofw --np 1 -D 31 -R 1 --local --mp 8.94535667698613,3.75120142793847 -a --trim3 0 --large-index --cp-min 2 --cp-ival 1 --mm -r -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1167s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '2' because it was < 2 characters long 1167s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '4' because it was < 2 characters long 1167s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '8' because it was < 2 characters long 1167s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '9' because it was < 2 characters long 1167s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read '17' because it was < 2 characters long 1167s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 1167s Warning: skipping read '20' because it was < 2 characters long 1167s 21 reads; of these: 1167s 21 (100.00%) were unpaired; of these: 1167s 21 (100.00%) aligned 0 times 1167s 0 (0.00%) aligned exactly 1 time 1167s 0 (0.00%) aligned >1 times 1167s 0.00% overall alignment rate 1167s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1167s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1167s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1167s Flattened IUPAC characters 1167s Mutating sequence Sim.pm.2 1167s Introducing 15 SNPs, 1/2 ref/read gaps, and 2 rearrangements 1167s Finished SNPs 1167s Finished ref gaps 1167s Finished read gaps 1167s Mutating sequence Sim.pm.1 1167s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1167s Finished SNPs 1167s Finished ref gaps 1167s Finished read gaps 1167s Mutated reference genome to subject genome 1167s SNPs introduced: 17 1167s Reference gaps introduced: 2 1167s Read gaps introduced: 2 1167s Rearrangements introduced: 2 1167s Created read sampler 1167s Sampling 96 reads 1167s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1167s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1167s *** Run 75 of 100 1167s /usr/bin/bowtie2 --cp-ival 3 --cp-min 4 --np 7 --large-index --ma 11.4516896341898 --score-min L,6.74626306045445,9.94153605123543 --trim5 8 --trim3 1 --mp 7.94882543042776,5.04363153302515 --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1167s parsing sequence Sim.pm.1... 1167s parsing sequence Sim.pm.2... 1167s Parsed 269 reference bases 1167s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 1167s 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 1167s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 1167s 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 1167s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 1167s 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 1167s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s 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 1167s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 1167s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 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 1167s 96 reads; of these: 1167s 96 (100.00%) were unpaired; of these: 1167s 74 (77.08%) aligned 0 times 1167s 6 (6.25%) aligned exactly 1 time 1167s 16 (16.67%) aligned >1 times 1167s 22.92% overall alignment rate 1167s Read 50 alignments... 1167s Read 100 alignments... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s ATGGACCACCTCGT 1167s ATGGACCACCTCGT 1167s Processing line... 1167s CGAGATGGACCACCTC 1167s CGAGATGGACCACCTC 1167s Processing line... 1167s CACATC 1167s CACATC 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s TG 1167s TG 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s GAGAC 1167s GAGAC 1167s Processing line... 1167s GAGAC 1167s GAGAC 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s CGCA 1167s CGCA 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s CACATCGAGATGGACCACCTC 1167s CACATCGAGATGGACCACCTC 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s ATTAGAGCTCGCAGCGCG 1167s ATTAGAGCTCGCAGCGCG 1167s Processing line... 1167s Processing line... 1167s CGAGATGGACCACCTC 1167s CGAGATGGACCACCTC 1167s Processing line... 1167s CATCGAG 1167s CATCGAG 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s AGAC 1167s AGAC 1167s Processing line... 1167s Processing line... 1167s CCACCT 1167s CCACCT 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s GG 1167s GG 1167s Processing line... 1167s AGCGC 1167s AGCGC 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s AGCCTGTCACATCGAGATGGAC 1167s AGCCTGTCACATCGAGATGGAC 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s AGATGGAC 1167s AGATGGAC 1167s Processing line... 1167s Processing line... 1167s ACGAGCCTGTCACATCGAGA 1167s ACGAGCCTGTCACATCGAGA 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s AGCCTG 1167s AGCCTG 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s CC 1167s CC 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s Processing line... 1167s GCAG 1167s GCAG 1167s Processing line... 1167s CGTGGG 1167s CGTGGG 1167s Processing line... 1167s --- Summary --- 1167s Read 1 reference strings 1167s Checked 22 alignments, 0 edits 1167s --------------- 1167s PASSED 1167s Flattened IUPAC characters 1167s Mutating sequence Sim.pm.2 1167s Introducing 17 SNPs, 1/2 ref/read gaps, and 0 rearrangements 1167s Finished SNPs 1167s Finished ref gaps 1167s Finished read gaps 1167s Mutating sequence Sim.pm.1 1167s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1167s Finished SNPs 1167s Finished ref gaps 1167s Finished read gaps 1167s Mutated reference genome to subject genome 1167s SNPs introduced: 19 1167s Reference gaps introduced: 1 1167s Read gaps introduced: 2 1167s Rearrangements introduced: 0 1167s Created read sampler 1167s Sampling 128 reads 1167s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1167s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1167s parsing sequence Sim.pm.1... 1167s parsing sequence Sim.pm.2... 1167s Parsed 269 reference bases 1167s *** Run 76 of 100 1167s /usr/bin/bowtie2 --rfg 3.2165755808395,5.28222354407842 --score-min L,1.94732079353289,2.6907039823522 -N 0 -L30 -D 17 --mp 5.31270588635467,4.06882265156597 --local --large-index --cp-min 3 --cp-ival 4 --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1168s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1168s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1168s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1168s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1168s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1168s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 1168s Read 50 alignments... 1168s Read 100 alignments... 1168s 128 reads; of these: 1168s 128 (100.00%) were unpaired; of these: 1168s 128 (100.00%) aligned 0 times 1168s 0 (0.00%) aligned exactly 1 time 1168s 0 (0.00%) aligned >1 times 1168s 0.00% overall alignment rate 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s --- Summary --- 1168s Read 1 reference strings 1168s Checked 0 alignments, 0 edits 1168s --------------- 1168s PASSED 1168s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1168s /usr/bin/bowtie2 --rfg 3.2165755808395,5.28222354407842 --score-min L,1.94732079353289,2.6907039823522 -N 0 -L30 -D 17 --mp 5.31270588635467,4.06882265156597 --local --large-index --cp-min 3 --cp-ival 4 --qseq -p 2 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1168s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 1168s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 1168s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 1168s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1168s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 1168s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (1) <= # seed mismatches (0) 1168s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 1168s 128 reads; of these: 1168s 128 (100.00%) were unpaired; of these: 1168s 128 (100.00%) aligned 0 times 1168s 0 (0.00%) aligned exactly 1 time 1168s 0 (0.00%) aligned >1 times 1168s 0.00% overall alignment rate 1168s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1168s Flattened IUPAC characters 1168s Mutating sequence Sim.pm.2 1168s Introducing 4 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1168s Finished SNPs 1168s Finished ref gaps 1168s Finished read gaps 1168s Mutating sequence Sim.pm.1 1168s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1168s Finished SNPs 1168s Finished ref gaps 1168s Finished read gaps 1168s Mutated reference genome to subject genome 1168s SNPs introduced: 9 1168s Reference gaps introduced: 0 1168s Read gaps introduced: 0 1168s Rearrangements introduced: 2 1168s Created read sampler 1168s Sampling 149 reads 1168s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1168s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1168s parsing sequence Sim.pm.1... 1168s parsing sequence Sim.pm.2... 1168s Parsed 269 reference bases 1168s *** Run 77 of 100 1168s /usr/bin/bowtie2 --trim5 6 --gbar 4 --score-min L,7.76561046022777,6.78390425286808 -R 1 --trim3 1 --local -M 4 --large-index --cp-min 2 --mm --cp-ival 2 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1168s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1168s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '21' because it was < 2 characters long 1168s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 1168s Warning: skipping read '23' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1168s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 1168s Warning: skipping read '51' because it was < 2 characters long 1168s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1168s Warning: skipping read '65' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '67' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '68' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '80' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '83' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1168s Read 50 alignments... 1168s Read 100 alignments... 1168s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '92' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '95' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '103' because it was < 2 characters long 1168s Read 150 alignments... 1168s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '119' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '125' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '126' because it was < 2 characters long 1168s Warning: skipping mate #2 of read '131' because length (1) <= # seed mismatches (0) 1168s Warning: skipping mate #2 of read '131' because it was < 2 characters long 1168s Warning: skipping mate #1 of read '144' because length (1) <= # seed mismatches (0) 1168s Warning: skipping mate #1 of read '144' because it was < 2 characters long 1168s 149 reads; of these: 1168s 122 (81.88%) were paired; of these: 1168s 122 (100.00%) aligned concordantly 0 times 1168s 0 (0.00%) aligned concordantly exactly 1 time 1168s 0 (0.00%) aligned concordantly >1 times 1168s ---- 1168s 122 pairs aligned concordantly 0 times; of these: 1168s 0 (0.00%) aligned discordantly 1 time 1168s ---- 1168s 122 pairs aligned 0 times concordantly or discordantly; of these: 1168s 244 mates make up the pairs; of these: 1168s 244 (100.00%) aligned 0 times 1168s 0 (0.00%) aligned exactly 1 time 1168s 0 (0.00%) aligned >1 times 1168s 27 (18.12%) were unpaired; of these: 1168s 27 (100.00%) aligned 0 times 1168s 0 (0.00%) aligned exactly 1 time 1168s 0 (0.00%) aligned >1 times 1168s 0.00% overall alignment rate 1168s Read 200 alignments... 1168s Read 250 alignments... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 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1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s Processing line... 1168s --- Summary --- 1168s Read 1 reference strings 1168s Checked 0 alignments, 0 edits 1168s --------------- 1168s PASSED 1168s Flattened IUPAC characters 1168s Mutating sequence Sim.pm.2 1168s Introducing 3 SNPs, 1/0 ref/read gaps, and 4 rearrangements 1168s Finished SNPs 1168s Finished ref gaps 1168s Finished read gaps 1168s Mutating sequence Sim.pm.1 1168s Introducing 5 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1168s Finished SNPs 1168s Finished ref gaps 1168s Finished read gaps 1168s Mutated reference genome to subject genome 1168s SNPs introduced: 8 1168s Reference gaps introduced: 2 1168s Read gaps introduced: 0 1168s Rearrangements introduced: 5 1168s Created read sampler 1168s Sampling 120 reads 1168s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1168s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1168s parsing sequence Sim.pm.1... 1168s parsing sequence Sim.pm.2... 1168s Parsed 269 reference bases 1168s *** Run 78 of 100 1168s /usr/bin/bowtie2 -D 3 --nofw --np 1 --n-ceil 1.11746969352706,0.0436987612463509 --score-min L,2.67893690043578,3.08114033979221 --rfg 38.8586061103183,16.8457629247056 --cp-ival 2 --cp-min 7 --large-index --trim3 4 --mp 7.22402371049021,3.89355595966441 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1169s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1169s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1169s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1169s Warning: skipping read '17' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1169s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1169s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1169s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1169s Read 50 alignments... 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1169s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1169s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '65' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1169s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1169s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '72' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1169s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1169s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1169s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1169s Warning: skipping mate #1 of read '111' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '111' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1169s Read 100 alignments... 1169s Read 150 alignments... 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1169s Read 200 alignments... 1169s 120 reads; of these: 1169s 113 (94.17%) were paired; of these: 1169s 108 (95.58%) aligned concordantly 0 times 1169s 0 (0.00%) aligned concordantly exactly 1 time 1169s 5 (4.42%) aligned concordantly >1 times 1169s ---- 1169s 108 pairs aligned concordantly 0 times; of these: 1169s 0 (0.00%) aligned discordantly 1 time 1169s ---- 1169s 108 pairs aligned 0 times concordantly or discordantly; of these: 1169s 216 mates make up the pairs; of these: 1169s 187 (86.57%) aligned 0 times 1169s 3 (1.39%) aligned exactly 1 time 1169s 26 (12.04%) aligned >1 times 1169s 7 (5.83%) were unpaired; of these: 1169s 7 (100.00%) aligned 0 times 1169s 0 (0.00%) aligned exactly 1 time 1169s 0 (0.00%) aligned >1 times 1169s 16.74% overall alignment rate 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s ACCA 1169s ACCA 1169s Processing line... 1169s CG 1169s CG 1169s Processing line... 1169s GAGGGTCGAG 1169s GAGGGTCGAG 1169s Processing line... 1169s Processing line... 1169s AGG 1169s AGG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s AGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGG 1169s AGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s AGAACACGAGCCTGTCACATCGAGATGGACCACCTC 1169s AGAACACGAGCCTGTCACATCGAGATGGACCACCTC 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s GT 1169s GT 1169s Processing line... 1169s Processing line... 1169s GCCTGTCA 1169s GCCTGTCA 1169s Processing line... 1169s CGAGCC 1169s CGAGCC 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s CGAGCCTGTCACATCG 1169s CGAGCCTGTCACATCG 1169s Processing line... 1169s CACATC 1169s CACATC 1169s Processing line... 1169s GG 1169s GG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s GA 1169s GA 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s CAC 1169s CAC 1169s Processing line... 1169s Processing line... 1169s GC 1169s GC 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s AG 1169s AG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s GAAC 1169s GAAC 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s GCCTGTCACATCGAGATGGACCACCTCGTG 1169s GCCTGTCACATCGAGATGGACCACCTCGTG 1169s Processing line... 1169s GAGAT 1169s GAGAT 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s GAGATGGA 1169s GAGATGGA 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s TGGACCACCTCG 1169s TGGACCACCTCG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s CACG 1169s CACG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s GTAGAACACGAGCCTGTC 1169s GTAGAACACGAGCCTGTC 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s GCCTGTCACATCGA 1169s GCCTGTCACATCGA 1169s Processing line... 1169s Processing line... 1169s CGAGCCTGTCACA 1169s CGAGCCTGTCACA 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s TAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGG 1169s TAGAACACGAGCCTGTCACATCGAGATGGACCACCTCGTGGG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s GGT 1169s GGT 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s AGTAGAACACGAGCCTGTCACATCGAG 1169s AGTAGAACACGAGCCTGTCACATCGAG 1169s Processing line... 1169s Processing line... 1169s ATTAGAGCTCG 1169s ATTAGAGCTCG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s /usr/bin/bowtie2 -D 3 --nofw --np 1 --n-ceil 1.11746969352706,0.0436987612463509 --score-min L,2.67893690043578,3.08114033979221 --rfg 38.8586061103183,16.8457629247056 --cp-ival 2 --cp-min 7 --large-index --trim3 4 --mp 7.22402371049021,3.89355595966441 -f -p 3 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1169s Processing line... 1169s GT 1169s GT 1169s Processing line... 1169s Processing line... 1169s CGAGATGGACC 1169s CGAGATGGACC 1169s Processing line... 1169s CACG 1169s CACG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s AGCCTGTCACATCGAGATGGACCACCTCGTG 1169s AGCCTGTCACATCGAGATGGACCACCTCGTG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s GGGTATGGTG 1169s GGGTATGGTG 1169s Processing line... 1169s Processing line... 1169s TAGAACACGAGCCTGTCACATCGAGA 1169s TAGAACACGAGCCTGTCACATCGAGA 1169s Processing line... 1169s GGT 1169s GGT 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s GAGCCTGTCACATCG 1169s GAGCCTGTCACATCG 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s Processing line... 1169s TGTCACATCGAGATGGACCACCTCGTG 1169s TGTCACATCGAGATGGACCACCTCGTG 1169s Processing line... 1169s Processing line... 1169s AGATGGACCACCTCGTGGG 1169s AGATGGACCACCTCGTGGG 1169s Processing line... 1169s --- Summary --- 1169s Read 1 reference strings 1169s Checked 39 alignments, 0 edits 1169s --------------- 1169s PASSED 1169s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1169s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1169s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1169s Warning: skipping read '17' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1169s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1169s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1169s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '65' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1169s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1169s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '72' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1169s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1169s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1169s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1169s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1169s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1169s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1169s Warning: skipping mate #1 of read '111' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '111' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1169s 120 reads; of these: 1169s 113 (94.17%) were paired; of these: 1169s 108 (95.58%) aligned concordantly 0 times 1169s 0 (0.00%) aligned concordantly exactly 1 time 1169s 5 (4.42%) aligned concordantly >1 times 1169s ---- 1169s 108 pairs aligned concordantly 0 times; of these: 1169s 0 (0.00%) aligned discordantly 1 time 1169s ---- 1169s 108 pairs aligned 0 times concordantly or discordantly; of these: 1169s 216 mates make up the pairs; of these: 1169s 187 (86.57%) aligned 0 times 1169s 3 (1.39%) aligned exactly 1 time 1169s 26 (12.04%) aligned >1 times 1169s 7 (5.83%) were unpaired; of these: 1169s 7 (100.00%) aligned 0 times 1169s 0 (0.00%) aligned exactly 1 time 1169s 0 (0.00%) aligned >1 times 1169s 16.74% overall alignment rate 1169s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1169s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1169s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1169s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1169s /usr/bin/bowtie2 -D 3 --nofw --np 1 --n-ceil 1.11746969352706,0.0436987612463509 --score-min L,2.67893690043578,3.08114033979221 --rfg 38.8586061103183,16.8457629247056 --cp-ival 2 --cp-min 7 --large-index --trim3 4 --mp 7.22402371049021,3.89355595966441 -f -p 2 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1169s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1169s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 1169s Warning: skipping read '17' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1169s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1169s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1169s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '43' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1169s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1169s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1169s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1169s Warning: skipping mate #1 of read '65' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1169s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '71' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1169s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '72' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1169s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1169s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1169s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '89' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1169s Warning: skipping mate #1 of read '111' because length (1) <= # seed mismatches (0) 1169s Warning: skipping mate #1 of read '111' because it was < 2 characters long 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1169s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1169s 120 reads; of these: 1169s 113 (94.17%) were paired; of these: 1169s 108 (95.58%) aligned concordantly 0 times 1169s 0 (0.00%) aligned concordantly exactly 1 time 1169s 5 (4.42%) aligned concordantly >1 times 1169s ---- 1169s 108 pairs aligned concordantly 0 times; of these: 1169s 0 (0.00%) aligned discordantly 1 time 1169s ---- 1169s 108 pairs aligned 0 times concordantly or discordantly; of these: 1169s 216 mates make up the pairs; of these: 1169s 187 (86.57%) aligned 0 times 1169s 3 (1.39%) aligned exactly 1 time 1169s 26 (12.04%) aligned >1 times 1169s 7 (5.83%) were unpaired; of these: 1169s 7 (100.00%) aligned 0 times 1169s 0 (0.00%) aligned exactly 1 time 1169s 0 (0.00%) aligned >1 times 1169s 16.74% overall alignment rate 1169s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1169s Flattened IUPAC characters 1169s Mutating sequence Sim.pm.1 1170s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1170s Finished SNPs 1170s Finished ref gaps 1170s Finished read gaps 1170s Mutating sequence Sim.pm.2 1170s Introducing 19 SNPs, 1/3 ref/read gaps, and 2 rearrangements 1170s Finished SNPs 1170s Finished ref gaps 1170s Finished read gaps 1170s Mutated reference genome to subject genome 1170s SNPs introduced: 25 1170s Reference gaps introduced: 1 1170s Read gaps introduced: 4 1170s Rearrangements introduced: 2 1170s Created read sampler 1170s Sampling 61 reads 1170s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1170s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1170s parsing sequence Sim.pm.1... 1170s parsing sequence Sim.pm.2... 1170s *** Run 79 of 100 1170s /usr/bin/bowtie2 -a --mp 8.27529353108255,1.91013349795777 --rdg 6.28313364045059 --score-min L,3.21153609546859,4.53048508897947 --large-index --cp-min 2 --cp-ival 1 --mm -N 1 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1170s Parsed 269 reference bases 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1170s Warning: skipping read '2' because length (1) <= # seed mismatches (1) 1170s Warning: skipping read '2' because it was < 2 characters long 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1170s Warning: skipping read '18' because length (1) <= # seed mismatches (1) 1170s Warning: skipping read '18' because it was < 2 characters long 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1170s Warning: skipping read '24' because length (1) <= # seed mismatches (1) 1170s Warning: skipping read '24' because it was < 2 characters long 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1170s Read 50 alignments... 1170s Read 100 alignments... 1170s 61 reads; of these: 1170s 61 (100.00%) were unpaired; of these: 1170s 47 (77.05%) aligned 0 times 1170s 1 (1.64%) aligned exactly 1 time 1170s 13 (21.31%) aligned >1 times 1170s 22.95% overall alignment rate 1170s Read 150 alignments... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s TGGACCACCTCG 1170s TGGACCACCTCG 1170s Processing line... 1170s TGGACCACCTCG 1170s TGGACCACCTCG 1170s Processing line... 1170s TGGACCACCTCG 1170s TGGACCACCTCG 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s GT 1170s GT 1170s Processing line... 1170s AC 1170s AC 1170s Processing line... 1170s Processing line... 1170s ATT 1170s ATT 1170s Processing line... 1170s AAT 1170s AAT 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s AAC 1170s AAC 1170s Processing line... 1170s AAC 1170s AAC 1170s Processing line... 1170s AAC 1170s AAC 1170s Processing line... 1170s AAC 1170s AAC 1170s Processing line... 1170s AAC 1170s AAC 1170s Processing line... 1170s AAC 1170s AAC 1170s Processing line... 1170s AAC 1170s AAC 1170s Processing line... 1170s AAC 1170s AAC 1170s Processing line... 1170s ATTAG 1170s ATTAG 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s CT 1170s CT 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s CT 1170s CT 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s CT 1170s CT 1170s Processing line... 1170s CT 1170s CT 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s CT 1170s CT 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s CT 1170s CT 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s CT 1170s CT 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s AG 1170s AG 1170s Processing line... 1170s CT 1170s CT 1170s Processing line... 1170s CT 1170s CT 1170s Processing line... 1170s CACGAGCCTGTCACATCG 1170s CACGAGCCTGTCACATCG 1170s Processing line... 1170s CACGAGCCTGTCACATCG 1170s CACGAGCCTGTCACATCG 1170s Processing line... 1170s CACGAGCCTGTCACATCG 1170s CACGAGCCTGTCACATCG 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s GCCT 1170s GCCT 1170s Processing line... 1170s GCCT 1170s GCCT 1170s Processing line... 1170s GCCT 1170s GCCT 1170s Processing line... 1170s CGAG 1170s CGAG 1170s Processing line... 1170s CTCG 1170s CTCG 1170s Processing line... 1170s CGAG 1170s CGAG 1170s Processing line... 1170s CTCG 1170s CTCG 1170s Processing line... 1170s CTCG 1170s CTCG 1170s Processing line... 1170s CGAG 1170s CGAG 1170s Processing line... 1170s CGAG 1170s CGAG 1170s Processing line... 1170s CTCG 1170s CTCG 1170s Processing line... 1170s CGAG 1170s CGAG 1170s Processing line... 1170s CGAG 1170s CGAG 1170s Processing line... 1170s CGAG 1170s CGAG 1170s Processing line... 1170s Processing line... 1170s ACCT 1170s ACCT 1170s Processing line... 1170s ACCT 1170s ACCT 1170s Processing line... 1170s ACCT 1170s ACCT 1170s Processing line... 1170s CGAGATG 1170s CGAGATG 1170s Processing line... 1170s CGAGATG 1170s CGAGATG 1170s Processing line... 1170s CGAGATG 1170s CGAGATG 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s CATCGAGATGGAC 1170s CATCGAGATGGAC 1170s Processing line... 1170s CATCGAGATGGAC 1170s CATCGAGATGGAC 1170s Processing line... 1170s CATCGAGATGGAC 1170s CATCGAGATGGAC 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s TAGAACACGAGCCTGT 1170s TAGAACACGAGCCTGT 1170s Processing line... 1170s TAGAACACGAGCCTGT 1170s TAGAACACGAGCCTGT 1170s Processing line... 1170s TAGAACACGAGCCTGT 1170s TAGAACACGAGCCTGT 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s TT 1170s TT 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s /usr/bin/bowtie2 -a --mp 8.27529353108255,1.91013349795777 --rdg 6.28313364045059 --score-min L,3.21153609546859,4.53048508897947 --large-index --cp-min 2 --cp-ival 1 --mm -N 1 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s Processing line... 1170s AA 1170s AA 1170s --- Summary --- 1170s Read 1 reference strings 1170s Checked 124 alignments, 0 edits 1170s --------------- 1170s PASSED 1170s ALSO checking that bowtie2 and bowtie2-align match up 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1170s Warning: skipping read '2' because length (1) <= # seed mismatches (1) 1170s Warning: skipping read '2' because it was < 2 characters long 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1170s Warning: skipping read '18' because length (1) <= # seed mismatches (1) 1170s Warning: skipping read '18' because it was < 2 characters long 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1170s Warning: skipping read '24' because length (1) <= # seed mismatches (1) 1170s Warning: skipping read '24' because it was < 2 characters long 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1170s 61 reads; of these: 1170s 61 (100.00%) were unpaired; of these: 1170s 47 (77.05%) aligned 0 times 1170s 1 (1.64%) aligned exactly 1 time 1170s 13 (21.31%) aligned >1 times 1170s 22.95% overall alignment rate 1170s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1170s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1170s /usr/bin/bowtie2 -a --mp 8.27529353108255,1.91013349795777 --rdg 6.28313364045059 --score-min L,3.21153609546859,4.53048508897947 --large-index --cp-min 2 --cp-ival 1 --mm -N 1 -f -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1170s Warning: skipping read '2' because length (1) <= # seed mismatches (1) 1170s Warning: skipping read '2' because it was < 2 characters long 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1170s Warning: skipping read '18' because length (1) <= # seed mismatches (1) 1170s Warning: skipping read '18' because it was < 2 characters long 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1170s Warning: skipping read '24' because length (1) <= # seed mismatches (1) 1170s Warning: skipping read '24' because it was < 2 characters long 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1170s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1170s 61 reads; of these: 1170s 61 (100.00%) were unpaired; of these: 1170s 47 (77.05%) aligned 0 times 1170s 1 (1.64%) aligned exactly 1 time 1170s 13 (21.31%) aligned >1 times 1170s 22.95% overall alignment rate 1170s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1170s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1170s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1170s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1170s /usr/bin/bowtie2 -a --mp 8.27529353108255,1.91013349795777 --rdg 6.28313364045059 --score-min L,3.21153609546859,4.53048508897947 --large-index --cp-min 2 --cp-ival 1 --mm -N 1 -f -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1171s Warning: skipping read '2' because length (1) <= # seed mismatches (1) 1171s Warning: skipping read '2' because it was < 2 characters long 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1171s Warning: skipping read '18' because length (1) <= # seed mismatches (1) 1171s Warning: skipping read '18' because it was < 2 characters long 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1171s Warning: skipping read '24' because length (1) <= # seed mismatches (1) 1171s Warning: skipping read '24' because it was < 2 characters long 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1171s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1171s 61 reads; of these: 1171s 61 (100.00%) were unpaired; of these: 1171s 47 (77.05%) aligned 0 times 1171s 1 (1.64%) aligned exactly 1 time 1171s 13 (21.31%) aligned >1 times 1171s 22.95% overall alignment rate 1171s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1171s Flattened IUPAC characters 1171s Mutating sequence Sim.pm.1 1171s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1171s Finished SNPs 1171s Finished ref gaps 1171s Finished read gaps 1171s Mutating sequence Sim.pm.2 1171s Introducing 16 SNPs, 5/3 ref/read gaps, and 3 rearrangements 1171s Finished SNPs 1171s Finished ref gaps 1171s Finished read gaps 1171s Mutated reference genome to subject genome 1171s SNPs introduced: 16 1171s Reference gaps introduced: 5 1171s Read gaps introduced: 3 1171s Rearrangements introduced: 3 1171s Created read sampler 1171s Sampling 61 reads 1171s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1171s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1171s parsing sequence Sim.pm.1... 1171s parsing sequence Sim.pm.2... 1171s Parsed 269 reference bases 1171s *** Run 80 of 100 1171s /usr/bin/bowtie2 --score-min L,1.56396282787288,1.96599907759108 -i C,2.39535673456514,12.1240728621121 --trim5 7 -N 1 --norc --nofw --large-index -M 3 --local --rdg 34.7104794631669,15.5583269612201 --mp 8.20099866859843,4.39469245613965 --cp-ival 1 --cp-min 2 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1171s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1171s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 1171s Warning: skipping read '1' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1171s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1171s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (1) 1171s Warning: skipping mate #2 of read '16' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1171s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 1171s Warning: skipping read '28' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1171s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (1) 1171s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1171s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 1171s Warning: skipping read '49' because it was < 2 characters long 1171s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (1) 1171s Warning: skipping mate #2 of read '54' because it was < 2 characters long 1171s 61 reads; of these: 1171s 47 (77.05%) were paired; of these: 1171s 47 (100.00%) aligned concordantly 0 times 1171s 0 (0.00%) aligned concordantly exactly 1 time 1171s 0 (0.00%) aligned concordantly >1 times 1171s ---- 1171s 47 pairs aligned concordantly 0 times; of these: 1171s 0 (0.00%) aligned discordantly 1 time 1171s ---- 1171s 47 pairs aligned 0 times concordantly or discordantly; of these: 1171s 94 mates make up the pairs; of these: 1171s 94 (100.00%) aligned 0 times 1171s 0 (0.00%) aligned exactly 1 time 1171s 0 (0.00%) aligned >1 times 1171s 14 (22.95%) were unpaired; of these: 1171s 14 (100.00%) aligned 0 times 1171s 0 (0.00%) aligned exactly 1 time 1171s 0 (0.00%) aligned >1 times 1171s 0.00% overall alignment rate 1171s Read 50 alignments... 1171s Read 100 alignments... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s --- Summary --- 1171s Read 1 reference strings 1171s Checked 0 alignments, 0 edits 1171s --------------- 1171s PASSED 1171s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1171s /usr/bin/bowtie2 --score-min L,1.56396282787288,1.96599907759108 -i C,2.39535673456514,12.1240728621121 --trim5 7 -N 1 --norc --nofw --large-index -M 3 --local --rdg 34.7104794631669,15.5583269612201 --mp 8.20099866859843,4.39469245613965 --cp-ival 1 --cp-min 2 -q -p 2 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1171s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 1171s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 1171s Warning: skipping read '1' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '12' because it was < 2 characters long 1171s Warning: skipping mate #2 of read '12' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '14' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (1) 1171s Warning: skipping mate #2 of read '16' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1171s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 1171s Warning: skipping read '28' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '29' because it was < 2 characters long 1171s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 1171s Warning: skipping read '49' because it was < 2 characters long 1171s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (1) 1171s Warning: skipping mate #2 of read '54' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '45' because it was < 2 characters long 1171s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (1) 1171s Warning: skipping mate #2 of read '46' because it was < 2 characters long 1171s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (1) 1171s Warning: skipping mate #1 of read '47' because it was < 2 characters long 1171s 61 reads; of these: 1171s 47 (77.05%) were paired; of these: 1171s 47 (100.00%) aligned concordantly 0 times 1171s 0 (0.00%) aligned concordantly exactly 1 time 1171s 0 (0.00%) aligned concordantly >1 times 1171s ---- 1171s 47 pairs aligned concordantly 0 times; of these: 1171s 0 (0.00%) aligned discordantly 1 time 1171s ---- 1171s 47 pairs aligned 0 times concordantly or discordantly; of these: 1171s 94 mates make up the pairs; of these: 1171s 94 (100.00%) aligned 0 times 1171s 0 (0.00%) aligned exactly 1 time 1171s 0 (0.00%) aligned >1 times 1171s 14 (22.95%) were unpaired; of these: 1171s 14 (100.00%) aligned 0 times 1171s 0 (0.00%) aligned exactly 1 time 1171s 0 (0.00%) aligned >1 times 1171s 0.00% overall alignment rate 1171s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1171s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1171s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1171s Flattened IUPAC characters 1171s Mutating sequence Sim.pm.2 1171s Introducing 18 SNPs, 2/2 ref/read gaps, and 1 rearrangements 1171s Finished SNPs 1171s Finished ref gaps 1171s Finished read gaps 1171s Mutating sequence Sim.pm.1 1171s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1171s Finished SNPs 1171s Finished ref gaps 1171s Finished read gaps 1171s Mutated reference genome to subject genome 1171s SNPs introduced: 21 1171s Reference gaps introduced: 3 1171s Read gaps introduced: 2 1171s Rearrangements introduced: 2 1171s Created read sampler 1171s Sampling 22 reads 1171s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1171s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1171s parsing sequence Sim.pm.1... 1171s parsing sequence Sim.pm.2... 1171s Parsed 269 reference bases 1171s *** Run 81 of 100 1171s /usr/bin/bowtie2 --np 3 --cp-min 2 --cp-ival 1 --mm -i S,0.628089582262381 --local --rfg 45.3157210605388,9.48443457818448 --trim3 0 --score-min L,4.43033332404603,2.11825658942191 --n-ceil 0.747094413499825,0.0739701587182765 --large-index -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1171s 22 reads; of these: 1171s 22 (100.00%) were paired; of these: 1171s 22 (100.00%) aligned concordantly 0 times 1171s 0 (0.00%) aligned concordantly exactly 1 time 1171s 0 (0.00%) aligned concordantly >1 times 1171s ---- 1171s 22 pairs aligned concordantly 0 times; of these: 1171s 0 (0.00%) aligned discordantly 1 time 1171s ---- 1171s 22 pairs aligned 0 times concordantly or discordantly; of these: 1171s 44 mates make up the pairs; of these: 1171s 44 (100.00%) aligned 0 times 1171s 0 (0.00%) aligned exactly 1 time 1171s 0 (0.00%) aligned >1 times 1171s 0.00% overall alignment rate 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s Processing line... 1171s --- Summary --- 1171s Read 1 reference strings 1171s Checked 0 alignments, 0 edits 1171s --------------- 1171s PASSED 1171s Flattened IUPAC characters 1171s Mutating sequence Sim.pm.1 1171s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1171s Finished SNPs 1171s Finished ref gaps 1171s Finished read gaps 1171s Mutating sequence Sim.pm.2 1171s Introducing 40 SNPs, 0/1 ref/read gaps, and 1 rearrangements 1171s Finished SNPs 1171s Finished ref gaps 1171s Finished read gaps 1171s Mutated reference genome to subject genome 1171s SNPs introduced: 46 1171s Reference gaps introduced: 1 1171s Read gaps introduced: 1 1171s Rearrangements introduced: 1 1171s Created read sampler 1171s Sampling 123 reads 1171s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1171s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1171s parsing sequence Sim.pm.1... 1171s parsing sequence Sim.pm.2... 1171s Parsed 269 reference bases 1171s *** Run 82 of 100 1171s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 3 --large-index -k 6 --trim3 2 --rdg 38.1799430210586 -N 0 -L23 -D 46 --nofw --score-min L,3.36741148411761,1.8656743646517 --gbar 6 --trim5 5 -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1172s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '1' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1172s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '15' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1172s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '18' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1172s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '21' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1172s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '24' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1172s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '34' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1172s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '45' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1172s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '46' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1172s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '56' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1172s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '66' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1172s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '72' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1172s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '74' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1172s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '76' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1172s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '79' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1172s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '89' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1172s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '92' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1172s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '94' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1172s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '95' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1172s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '96' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1172s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '98' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1172s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '105' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1172s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '110' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1172s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '112' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1172s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '113' because it was < 2 characters long 1172s Read 50 alignments... 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1172s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '121' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1172s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '123' because it was < 2 characters long 1172s Read 100 alignments... 1172s 123 reads; of these: 1172s 123 (100.00%) were unpaired; of these: 1172s 113 (91.87%) aligned 0 times 1172s 1 (0.81%) aligned exactly 1 time 1172s 9 (7.32%) aligned >1 times 1172s 8.13% overall alignment rate 1172s Read 150 alignments... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s GCC 1172s GCC 1172s Processing line... 1172s GCC 1172s GCC 1172s Processing line... 1172s GCC 1172s GCC 1172s Processing line... 1172s Processing line... 1172s CA 1172s CA 1172s Processing line... 1172s CA 1172s CA 1172s Processing line... 1172s CA 1172s CA 1172s Processing line... 1172s CA 1172s CA 1172s Processing line... 1172s CA 1172s CA 1172s Processing line... 1172s CA 1172s CA 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s CT 1172s CT 1172s Processing line... 1172s CT 1172s CT 1172s Processing line... 1172s CT 1172s CT 1172s Processing line... 1172s CT 1172s CT 1172s Processing line... 1172s CT 1172s CT 1172s Processing line... 1172s CT 1172s CT 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s TGGA 1172s TGGA 1172s Processing line... 1172s TGGA 1172s TGGA 1172s Processing line... 1172s TGGA 1172s TGGA 1172s Processing line... 1172s TGGA 1172s TGGA 1172s Processing line... 1172s TGGA 1172s TGGA 1172s Processing line... 1172s TGGA 1172s TGGA 1172s Processing line... 1172s Processing line... 1172s CACG 1172s CACG 1172s Processing line... 1172s CACG 1172s CACG 1172s Processing line... 1172s CACG 1172s CACG 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s GATA 1172s GATA 1172s Processing line... 1172s GATA 1172s GATA 1172s Processing line... 1172s GATA 1172s GATA 1172s Processing line... 1172s GATA 1172s GATA 1172s Processing line... 1172s GATA 1172s GATA 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s AT 1172s AT 1172s Processing line... 1172s AT 1172s AT 1172s Processing line... 1172s AT 1172s AT 1172s Processing line... 1172s AT 1172s AT 1172s Processing line... 1172s AT 1172s AT 1172s Processing line... 1172s AT 1172s AT 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s GTATGGTGAGGGTCGA 1172s GTATGGTGAGGGTCGA 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s AGA 1172s AGA 1172s Processing line... 1172s AGA 1172s AGA 1172s Processing line... 1172s AGA 1172s AGA 1172s Processing line... 1172s AGA 1172s AGA 1172s Processing line... 1172s AGA 1172s AGA 1172s Processing line... 1172s AGA 1172s AGA 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s ACC 1172s ACC 1172s Processing line... 1172s ACC 1172s ACC 1172s Processing line... 1172s ACC 1172s ACC 1172s Processing line... 1172s ACC 1172s ACC 1172s Processing line... 1172s ACC 1172s ACC 1172s Processing line... 1172s ACC 1172s ACC 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s --- Summary --- 1172s Read 1 reference strings 1172s Checked 48 alignments, 0 edits 1172s --------------- 1172s PASSED 1172s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1172s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 3 --large-index -k 6 --trim3 2 --rdg 38.1799430210586 -N 0 -L23 -D 46 --nofw --score-min L,3.36741148411761,1.8656743646517 --gbar 6 --trim5 5 -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1172s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '1' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1172s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '15' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1172s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '18' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1172s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '21' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1172s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '24' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1172s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '34' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1172s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '56' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1172s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '66' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1172s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '45' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1172s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '46' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1172s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '72' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1172s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '74' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1172s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '76' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1172s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '89' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1172s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '92' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1172s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '94' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1172s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '95' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1172s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '96' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1172s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '98' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 1172s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '113' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 1172s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '121' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 1172s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '123' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1172s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '79' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1172s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '105' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 1172s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '110' because it was < 2 characters long 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 1172s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 1172s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '112' because it was < 2 characters long 1172s 123 reads; of these: 1172s 123 (100.00%) were unpaired; of these: 1172s 113 (91.87%) aligned 0 times 1172s 1 (0.81%) aligned exactly 1 time 1172s 9 (7.32%) aligned >1 times 1172s 8.13% overall alignment rate 1172s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1172s Flattened IUPAC characters 1172s Mutating sequence Sim.pm.1 1172s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1172s Finished SNPs 1172s Finished ref gaps 1172s Finished read gaps 1172s Mutating sequence Sim.pm.2 1172s Introducing 0 SNPs, 4/1 ref/read gaps, and 1 rearrangements 1172s Finished SNPs 1172s Finished ref gaps 1172s Finished read gaps 1172s Mutated reference genome to subject genome 1172s SNPs introduced: 5 1172s Reference gaps introduced: 4 1172s Read gaps introduced: 2 1172s Rearrangements introduced: 1 1172s Created read sampler 1172s Sampling 173 reads 1172s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1172s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1172s parsing sequence Sim.pm.1... 1172s parsing sequence Sim.pm.2... 1172s *** Run 83 of 100 1172s /usr/bin/bowtie2 --cp-min 4 --mm --cp-ival 1 --rdg 13.7426103936145,19.3749080001689 -a --local --large-index --norc --np 6 -D 35 -R 3 --trim5 5 --rfg 36.8320680850771 --gbar 1 --score-min L,8.02847430502079,7.60699011552807 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1172s Parsed 269 reference bases 1172s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '7' because it was < 2 characters long 1172s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '8' because it was < 2 characters long 1172s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '20' because it was < 2 characters long 1172s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '24' because it was < 2 characters long 1172s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '33' because it was < 2 characters long 1172s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '36' because it was < 2 characters long 1172s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '50' because it was < 2 characters long 1172s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '54' because it was < 2 characters long 1172s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '64' because it was < 2 characters long 1172s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '65' because it was < 2 characters long 1172s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '66' because it was < 2 characters long 1172s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '71' because it was < 2 characters long 1172s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '74' because it was < 2 characters long 1172s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '79' because it was < 2 characters long 1172s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '81' because it was < 2 characters long 1172s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '96' because it was < 2 characters long 1172s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '99' because it was < 2 characters long 1172s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '105' because it was < 2 characters long 1172s Warning: skipping read '106' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '106' because it was < 2 characters long 1172s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '116' because it was < 2 characters long 1172s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '117' because it was < 2 characters long 1172s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '125' because it was < 2 characters long 1172s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '126' because it was < 2 characters long 1172s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '127' because it was < 2 characters long 1172s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '135' because it was < 2 characters long 1172s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '138' because it was < 2 characters long 1172s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '140' because it was < 2 characters long 1172s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '142' because it was < 2 characters long 1172s Warning: skipping read '148' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '148' because it was < 2 characters long 1172s Warning: skipping read '155' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '155' because it was < 2 characters long 1172s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '156' because it was < 2 characters long 1172s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '158' because it was < 2 characters long 1172s Warning: skipping read '162' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '162' because it was < 2 characters long 1172s Warning: skipping read '164' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '164' because it was < 2 characters long 1172s Read 50 alignments... 1172s 173 reads; of these: 1172s 173 (100.00%) were unpaired; of these: 1172s 173 (100.00%) aligned 0 times 1172s 0 (0.00%) aligned exactly 1 time 1172s 0 (0.00%) aligned >1 times 1172s 0.00% overall alignment rate 1172s Read 100 alignments... 1172s Read 150 alignments... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s Processing line... 1172s --- Summary --- 1172s Read 1 reference strings 1172s Checked 0 alignments, 0 edits 1172s --------------- 1172s PASSED 1172s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1172s /usr/bin/bowtie2 --cp-min 4 --mm --cp-ival 1 --rdg 13.7426103936145,19.3749080001689 -a --local --large-index --norc --np 6 -D 35 -R 3 --trim5 5 --rfg 36.8320680850771 --gbar 1 --score-min L,8.02847430502079,7.60699011552807 -f -p 2 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1172s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '7' because it was < 2 characters long 1172s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '8' because it was < 2 characters long 1172s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '20' because it was < 2 characters long 1172s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '24' because it was < 2 characters long 1172s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '33' because it was < 2 characters long 1172s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '36' because it was < 2 characters long 1172s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '65' because it was < 2 characters long 1172s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '66' because it was < 2 characters long 1172s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '71' because it was < 2 characters long 1172s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '74' because it was < 2 characters long 1172s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '79' because it was < 2 characters long 1172s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '81' because it was < 2 characters long 1172s Warning: skipping read '50' because it was < 2 characters long 1172s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '54' because it was < 2 characters long 1172s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '64' because it was < 2 characters long 1172s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '99' because it was < 2 characters long 1172s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '105' because it was < 2 characters long 1172s Warning: skipping read '106' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '106' because it was < 2 characters long 1172s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '116' because it was < 2 characters long 1172s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '117' because it was < 2 characters long 1172s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '125' because it was < 2 characters long 1172s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '96' because it was < 2 characters long 1172s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '135' because it was < 2 characters long 1172s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '138' because it was < 2 characters long 1172s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '140' because it was < 2 characters long 1172s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '142' because it was < 2 characters long 1172s Warning: skipping read '148' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '148' because it was < 2 characters long 1172s Warning: skipping read '155' because length (1) <= # seed mismatches (0) 1172s Warning: skipping read '155' because it was < 2 characters long 1172s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '156' because it was < 2 characters long 1172s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '158' because it was < 2 characters long 1172s Warning: skipping read '162' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '162' because it was < 2 characters long 1172s Warning: skipping read '164' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '164' because it was < 2 characters long 1172s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '126' because it was < 2 characters long 1172s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 1172s Warning: skipping read '127' because it was < 2 characters long 1172s 173 reads; of these: 1172s 173 (100.00%) were unpaired; of these: 1172s 173 (100.00%) aligned 0 times 1172s 0 (0.00%) aligned exactly 1 time 1172s 0 (0.00%) aligned >1 times 1172s 0.00% overall alignment rate 1172s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1173s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1173s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1173s Flattened IUPAC characters 1173s Mutating sequence Sim.pm.1 1173s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 1173s Finished SNPs 1173s Finished ref gaps 1173s Finished read gaps 1173s Mutating sequence Sim.pm.2 1173s Introducing 9 SNPs, 2/1 ref/read gaps, and 1 rearrangements 1173s Finished SNPs 1173s Finished ref gaps 1173s Finished read gaps 1173s Mutated reference genome to subject genome 1173s SNPs introduced: 9 1173s Reference gaps introduced: 3 1173s Read gaps introduced: 2 1173s Rearrangements introduced: 1 1173s Created read sampler 1173s Sampling 107 reads 1173s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1173s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1173s parsing sequence Sim.pm.1... 1173s parsing sequence Sim.pm.2... 1173s Parsed 269 reference bases 1173s *** Run 84 of 100 1173s /usr/bin/bowtie2 --rdg 46.0690636191845,7.40500942590917 -k 7 --large-index --cp-min 4 --cp-ival 3 --trim5 8 --score-min L,4.71777805639949,2.55388099983329 --norc -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1173s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1173s Warning: skipping read '2' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1173s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 1173s Warning: skipping read '3' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1173s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '4' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1173s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '16' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1173s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '29' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1173s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '33' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1173s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '34' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1173s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '41' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1173s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '46' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1173s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '49' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1173s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '52' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1173s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '57' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1173s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '65' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1173s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '71' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1173s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '87' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1173s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '89' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1173s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '96' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1173s 107 reads; of these: 1173s 107 (100.00%) were unpaired; of these: 1173s 98 (91.59%) aligned 0 times 1173s 3 (2.80%) aligned exactly 1 time 1173s 6 (5.61%) aligned >1 times 1173s 8.41% overall alignment rate 1173s Read 50 alignments... 1173s Read 100 alignments... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s CA 1173s CA 1173s Processing line... 1173s CA 1173s CA 1173s Processing line... 1173s CA 1173s CA 1173s Processing line... 1173s CA 1173s CA 1173s Processing line... 1173s CA 1173s CA 1173s Processing line... 1173s CA 1173s CA 1173s Processing line... 1173s CA 1173s CA 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s TCGAGG 1173s TCGAGG 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s GGGT 1173s GGGT 1173s Processing line... 1173s GGGT 1173s GGGT 1173s Processing line... 1173s TGTCACATCGAGATGG 1173s TGTCACATCGAGATGG 1173s Processing line... 1173s TGTCACATCGAGATGG 1173s TGTCACATCGAGATGG 1173s Processing line... 1173s TGTCACATCGAGATGG 1173s TGTCACATCGAGATGG 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s GATG 1173s GATG 1173s Processing line... 1173s GATG 1173s GATG 1173s Processing line... 1173s GATG 1173s GATG 1173s Processing line... 1173s TAACCAAAAC 1173s TAACCAAAAC 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s GTGGCTGA 1173s GTGGCTGA 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s TC 1173s TC 1173s Processing line... 1173s /usr/bin/bowtie2 --rdg 46.0690636191845,7.40500942590917 -k 7 --large-index --cp-min 4 --cp-ival 3 --trim5 8 --score-min L,4.71777805639949,2.55388099983329 --norc -f -p 3 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1173s TC 1173s TC 1173s Processing line... 1173s TC 1173s TC 1173s Processing line... 1173s TC 1173s TC 1173s Processing line... 1173s TC 1173s TC 1173s Processing line... 1173s TC 1173s TC 1173s Processing line... 1173s TC 1173s TC 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s AG 1173s AG 1173s Processing line... 1173s AG 1173s AG 1173s Processing line... 1173s AG 1173s AG 1173s Processing line... 1173s AG 1173s AG 1173s Processing line... 1173s AG 1173s AG 1173s Processing line... 1173s AG 1173s AG 1173s Processing line... 1173s AG 1173s AG 1173s --- Summary --- 1173s Read 1 reference strings 1173s Checked 32 alignments, 0 edits 1173s --------------- 1173s PASSED 1173s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1173s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 1173s Warning: skipping read '2' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1173s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 1173s Warning: skipping read '3' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1173s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '4' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1173s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '16' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1173s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '33' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1173s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '29' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1173s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '49' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1173s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '52' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1173s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '57' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1173s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '65' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1173s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '71' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1173s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '34' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1173s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '41' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1173s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '46' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1173s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '87' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1173s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '89' because it was < 2 characters long 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1173s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1173s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 1173s Warning: skipping read '96' because it was < 2 characters long 1173s 107 reads; of these: 1173s 107 (100.00%) were unpaired; of these: 1173s 98 (91.59%) aligned 0 times 1173s 3 (2.80%) aligned exactly 1 time 1173s 6 (5.61%) aligned >1 times 1173s 8.41% overall alignment rate 1173s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1173s Flattened IUPAC characters 1173s Mutating sequence Sim.pm.2 1173s Introducing 10 SNPs, 1/0 ref/read gaps, and 1 rearrangements 1173s Finished SNPs 1173s Finished ref gaps 1173s Finished read gaps 1173s Mutating sequence Sim.pm.1 1173s Introducing 2 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1173s Finished SNPs 1173s Finished ref gaps 1173s Finished read gaps 1173s Mutated reference genome to subject genome 1173s SNPs introduced: 12 1173s Reference gaps introduced: 1 1173s Read gaps introduced: 0 1173s Rearrangements introduced: 3 1173s Created read sampler 1173s Sampling 50 reads 1173s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1173s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1173s parsing sequence Sim.pm.1... 1173s parsing sequence Sim.pm.2... 1173s Parsed 269 reference bases 1173s *** Run 85 of 100 1173s /usr/bin/bowtie2 --score-min L,4.9648864329864,3.64164359147647 --n-ceil 0.610281292290385,0.399208391752426 --rfg 23.0605441197503 --trim5 2 -N 1 --np 3 --large-index --local --trim3 1 -a --cp-ival 1 --cp-min 2 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq 1173s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 1173s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1173s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (1) 1173s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1173s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (1) 1173s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1173s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (1) 1173s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1173s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 1173s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1173s 50 reads; of these: 1173s 46 (92.00%) were paired; of these: 1173s 46 (100.00%) aligned concordantly 0 times 1173s 0 (0.00%) aligned concordantly exactly 1 time 1173s 0 (0.00%) aligned concordantly >1 times 1173s ---- 1173s 46 pairs aligned concordantly 0 times; of these: 1173s 0 (0.00%) aligned discordantly 1 time 1173s ---- 1173s 46 pairs aligned 0 times concordantly or discordantly; of these: 1173s 92 mates make up the pairs; of these: 1173s 92 (100.00%) aligned 0 times 1173s 0 (0.00%) aligned exactly 1 time 1173s 0 (0.00%) aligned >1 times 1173s 4 (8.00%) were unpaired; of these: 1173s 4 (100.00%) aligned 0 times 1173s 0 (0.00%) aligned exactly 1 time 1173s 0 (0.00%) aligned >1 times 1173s 0.00% overall alignment rate 1173s Read 50 alignments... 1173s Read 100 alignments... 1173s /usr/bin/bowtie2 --score-min L,4.9648864329864,3.64164359147647 --n-ceil 0.610281292290385,0.399208391752426 --rfg 23.0605441197503 --trim5 2 -N 1 --np 3 --large-index --local --trim3 1 -a --cp-ival 1 --cp-min 2 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s Processing line... 1173s --- Summary --- 1173s Read 1 reference strings 1173s Checked 0 alignments, 0 edits 1173s --------------- 1173s PASSED 1173s ALSO checking that bowtie2 and bowtie2-align match up 1174s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 1174s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1174s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (1) 1174s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1174s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (1) 1174s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1174s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (1) 1174s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1174s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 1174s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1174s 50 reads; of these: 1174s 46 (92.00%) were paired; of these: 1174s 46 (100.00%) aligned concordantly 0 times 1174s 0 (0.00%) aligned concordantly exactly 1 time 1174s 0 (0.00%) aligned concordantly >1 times 1174s ---- 1174s 46 pairs aligned concordantly 0 times; of these: 1174s 0 (0.00%) aligned discordantly 1 time 1174s ---- 1174s 46 pairs aligned 0 times concordantly or discordantly; of these: 1174s 92 mates make up the pairs; of these: 1174s 92 (100.00%) aligned 0 times 1174s 0 (0.00%) aligned exactly 1 time 1174s 0 (0.00%) aligned >1 times 1174s 4 (8.00%) were unpaired; of these: 1174s 4 (100.00%) aligned 0 times 1174s 0 (0.00%) aligned exactly 1 time 1174s 0 (0.00%) aligned >1 times 1174s 0.00% overall alignment rate 1174s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1174s /usr/bin/bowtie2 --score-min L,4.9648864329864,3.64164359147647 --n-ceil 0.610281292290385,0.399208391752426 --rfg 23.0605441197503 --trim5 2 -N 1 --np 3 --large-index --local --trim3 1 -a --cp-ival 1 --cp-min 2 --qseq -p 4 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1174s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1174s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 1174s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 1174s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (1) 1174s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 1174s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (1) 1174s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1174s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (1) 1174s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 1174s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 1174s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 1174s 50 reads; of these: 1174s 46 (92.00%) were paired; of these: 1174s 46 (100.00%) aligned concordantly 0 times 1174s 0 (0.00%) aligned concordantly exactly 1 time 1174s 0 (0.00%) aligned concordantly >1 times 1174s ---- 1174s 46 pairs aligned concordantly 0 times; of these: 1174s 0 (0.00%) aligned discordantly 1 time 1174s ---- 1174s 46 pairs aligned 0 times concordantly or discordantly; of these: 1174s 92 mates make up the pairs; of these: 1174s 92 (100.00%) aligned 0 times 1174s 0 (0.00%) aligned exactly 1 time 1174s 0 (0.00%) aligned >1 times 1174s 4 (8.00%) were unpaired; of these: 1174s 4 (100.00%) aligned 0 times 1174s 0 (0.00%) aligned exactly 1 time 1174s 0 (0.00%) aligned >1 times 1174s 0.00% overall alignment rate 1174s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1174s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1174s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1174s Flattened IUPAC characters 1174s Mutating sequence Sim.pm.2 1174s Introducing 2 SNPs, 1/0 ref/read gaps, and 2 rearrangements 1174s Finished SNPs 1174s Finished ref gaps 1174s Finished read gaps 1174s Mutating sequence Sim.pm.1 1174s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1174s Finished SNPs 1174s Finished ref gaps 1174s Finished read gaps 1174s Mutated reference genome to subject genome 1174s SNPs introduced: 6 1174s Reference gaps introduced: 1 1174s Read gaps introduced: 0 1174s Rearrangements introduced: 2 1174s Created read sampler 1174s Sampling 53 reads 1174s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1174s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1174s parsing sequence Sim.pm.1... 1174s parsing sequence Sim.pm.2... 1174s Parsed 269 reference bases 1174s *** Run 86 of 100 1174s /usr/bin/bowtie2 --cp-ival 1 --cp-min 12 --large-index --mp 6.1185564934636,2.8368258905272 --local -N 0 -L14 -D 15 --score-min L,1.00399802966967,2.22080626188243 --rfg 12.4969533887883 -i L,0.429652968431126 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1174s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 1174s Warning: skipping mate #2 of read '22' because it was < 2 characters long 1174s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 1174s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1174s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 1174s Warning: skipping mate #2 of read '32' because it was < 2 characters long 1174s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 1174s Warning: skipping mate #2 of read '43' because it was < 2 characters long 1174s 53 reads; of these: 1174s 53 (100.00%) were paired; of these: 1174s 53 (100.00%) aligned concordantly 0 times 1174s 0 (0.00%) aligned concordantly exactly 1 time 1174s 0 (0.00%) aligned concordantly >1 times 1174s ---- 1174s 53 pairs aligned concordantly 0 times; of these: 1174s 0 (0.00%) aligned discordantly 1 time 1174s ---- 1174s 53 pairs aligned 0 times concordantly or discordantly; of these: 1174s 106 mates make up the pairs; of these: 1174s 106 (100.00%) aligned 0 times 1174s 0 (0.00%) aligned exactly 1 time 1174s 0 (0.00%) aligned >1 times 1174s 0.00% overall alignment rate 1174s Read 50 alignments... 1174s Read 100 alignments... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s Processing line... 1174s --- Summary --- 1174s Read 1 reference strings 1174s Checked 0 alignments, 0 edits 1174s --------------- 1174s PASSED 1174s ALSO checking that bowtie2 and bowtie2-align match up 1174s /usr/bin/bowtie2 --cp-ival 1 --cp-min 12 --large-index --mp 6.1185564934636,2.8368258905272 --local -N 0 -L14 -D 15 --score-min L,1.00399802966967,2.22080626188243 --rfg 12.4969533887883 -i L,0.429652968431126 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1175s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 1175s Warning: skipping mate #2 of read '22' because it was < 2 characters long 1175s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 1175s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1175s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 1175s Warning: skipping mate #2 of read '32' because it was < 2 characters long 1175s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 1175s Warning: skipping mate #2 of read '43' because it was < 2 characters long 1175s 53 reads; of these: 1175s 53 (100.00%) were paired; of these: 1175s 53 (100.00%) aligned concordantly 0 times 1175s 0 (0.00%) aligned concordantly exactly 1 time 1175s 0 (0.00%) aligned concordantly >1 times 1175s ---- 1175s 53 pairs aligned concordantly 0 times; of these: 1175s 0 (0.00%) aligned discordantly 1 time 1175s ---- 1175s 53 pairs aligned 0 times concordantly or discordantly; of these: 1175s 106 mates make up the pairs; of these: 1175s 106 (100.00%) aligned 0 times 1175s 0 (0.00%) aligned exactly 1 time 1175s 0 (0.00%) aligned >1 times 1175s 0.00% overall alignment rate 1175s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1175s Flattened IUPAC characters 1175s Mutating sequence Sim.pm.2 1175s Introducing 17 SNPs, 2/0 ref/read gaps, and 0 rearrangements 1175s Finished SNPs 1175s Finished ref gaps 1175s Finished read gaps 1175s Mutating sequence Sim.pm.1 1175s Introducing 9 SNPs, 0/2 ref/read gaps, and 1 rearrangements 1175s Finished SNPs 1175s Finished ref gaps 1175s Finished read gaps 1175s Mutated reference genome to subject genome 1175s SNPs introduced: 26 1175s Reference gaps introduced: 2 1175s Read gaps introduced: 2 1175s Rearrangements introduced: 1 1175s Created read sampler 1175s Sampling 56 reads 1175s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1175s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1175s parsing sequence Sim.pm.1... 1175s parsing sequence Sim.pm.2... 1175s Parsed 269 reference bases 1175s *** Run 87 of 100 1175s /usr/bin/bowtie2 --local --large-index --cp-min 2 --mm --cp-ival 3 --trim5 0 --gbar 1 --score-min L,1.69191323444835,3.25555650318149 --norc --np 3 -N 1 -L28 -R 3 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1175s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 1175s Warning: skipping read '8' because it was < 2 characters long 1175s Warning: skipping read '21' because length (1) <= # seed mismatches (1) 1175s Warning: skipping read '21' because it was < 2 characters long 1175s Warning: skipping read '27' because length (1) <= # seed mismatches (1) 1175s Warning: skipping read '27' because it was < 2 characters long 1175s 56 reads; of these: 1175s 56 (100.00%) were unpaired; of these: 1175s 56 (100.00%) aligned 0 times 1175s 0 (0.00%) aligned exactly 1 time 1175s 0 (0.00%) aligned >1 times 1175s 0.00% overall alignment rate 1175s Read 50 alignments... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s Processing line... 1175s --- Summary --- 1175s Read 1 reference strings 1175s Checked 0 alignments, 0 edits 1175s --------------- 1175s PASSED 1175s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1175s /usr/bin/bowtie2 --local --large-index --cp-min 2 --mm --cp-ival 3 --trim5 0 --gbar 1 --score-min L,1.69191323444835,3.25555650318149 --norc --np 3 -N 1 -L28 -R 3 -f -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1175s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 1175s Warning: skipping read '8' because it was < 2 characters long 1175s Warning: skipping read '21' because length (1) <= # seed mismatches (1) 1175s Warning: skipping read '21' because it was < 2 characters long 1175s Warning: skipping read '27' because length (1) <= # seed mismatches (1) 1175s Warning: skipping read '27' because it was < 2 characters long 1175s 56 reads; of these: 1175s 56 (100.00%) were unpaired; of these: 1175s 56 (100.00%) aligned 0 times 1175s 0 (0.00%) aligned exactly 1 time 1175s 0 (0.00%) aligned >1 times 1175s 0.00% overall alignment rate 1175s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1175s *** Run 88 of 100 1175s /usr/bin/bowtie2 -R 1 -D 33 --score-min L,4.31661143336071,9.00034418098128 --cp-ival 1 --cp-min 4 --large-index --ma 32.2894374931241 -a --mp 5.51515988576626,1.05013603310174 --rdg 44.1521308193594 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1175s Flattened IUPAC characters 1175s Mutating sequence Sim.pm.1 1175s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1175s Finished SNPs 1175s Finished ref gaps 1175s Finished read gaps 1175s Mutating sequence Sim.pm.2 1175s Introducing 7 SNPs, 1/3 ref/read gaps, and 2 rearrangements 1175s Finished SNPs 1175s Finished ref gaps 1175s Finished read gaps 1175s Mutated reference genome to subject genome 1175s SNPs introduced: 11 1175s Reference gaps introduced: 1 1175s Read gaps introduced: 3 1175s Rearrangements introduced: 2 1175s Created read sampler 1175s Sampling 174 reads 1175s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1175s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1175s parsing sequence Sim.pm.1... 1175s parsing sequence Sim.pm.2... 1175s Parsed 269 reference bases 1175s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1175s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1175s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1175s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1175s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1175s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1175s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1176s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '13' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1176s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '15' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1176s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '28' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1176s Read 50 alignments... 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1176s Read 100 alignments... 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1176s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1176s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1176s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '62' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1176s Read 150 alignments... 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1176s Warning: skipping mate #2 of read '96' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '96' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1176s Warning: skipping mate #1 of read '102' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #1 of read '102' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1176s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '103' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1176s Read 200 alignments... 1176s Read 250 alignments... 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 1176s Warning: skipping mate #2 of read '126' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '126' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 1176s Read 300 alignments... 1176s Read 350 alignments... 1176s Read 400 alignments... 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 1176s Warning: skipping mate #2 of read '151' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '151' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 1176s Read 450 alignments... 1176s Read 500 alignments... 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 1176s 174 reads; of these: 1176s 174 (100.00%) were paired; of these: 1176s 167 (95.98%) aligned concordantly 0 times 1176s 0 (0.00%) aligned concordantly exactly 1 time 1176s 7 (4.02%) aligned concordantly >1 times 1176s ---- 1176s 167 pairs aligned concordantly 0 times; of these: 1176s 0 (0.00%) aligned discordantly 1 time 1176s ---- 1176s 167 pairs aligned 0 times concordantly or discordantly; of these: 1176s 334 mates make up the pairs; of these: 1176s 287 (85.93%) aligned 0 times 1176s 7 (2.10%) aligned exactly 1 time 1176s 40 (11.98%) aligned >1 times 1176s 17.53% overall alignment rate 1176s Read 550 alignments... 1176s Read 600 alignments... 1176s Read 650 alignments... 1176s Read 700 alignments... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GAAA 1176s GAAA 1176s Processing line... 1176s AGAACACGA 1176s AGAACACGA 1176s Processing line... 1176s AGAACACGA 1176s AGAACACGA 1176s Processing line... 1176s AGAACACGA 1176s AGAACACGA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s CTCGTG 1176s CTCGTG 1176s Processing line... 1176s CTCGTG 1176s CTCGTG 1176s Processing line... 1176s CACGAG 1176s CACGAG 1176s Processing line... 1176s CACGAG 1176s CACGAG 1176s Processing line... 1176s CTCGTG 1176s CTCGTG 1176s Processing line... 1176s CACGAG 1176s CACGAG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s TT 1176s TT 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s Processing line... 1176s TGTCA 1176s TGTCA 1176s Processing line... 1176s TGTCA 1176s TGTCA 1176s Processing line... 1176s TGTCA 1176s TGTCA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GATGGACCACCTCGTG 1176s GATGGACCACCTCGTG 1176s Processing line... 1176s GATGGACCACCTCGTG 1176s GATGGACCACCTCGTG 1176s Processing line... 1176s GATGGACCACCTCGTG 1176s GATGGACCACCTCGTG 1176s Processing line... 1176s Processing line... 1176s AGTAGAACACGAGCCTGTCACATCG 1176s AGTAGAACACGAGCCTGTCACATCG 1176s Processing line... 1176s AGTAGAACACGAGCCTGTCACATCG 1176s AGTAGAACACGAGCCTGTCACATCG 1176s Processing line... 1176s AGTAGAACACGAGCCTGTCACATCG 1176s AGTAGAACACGAGCCTGTCACATCG 1176s Processing line... 1176s Processing line... 1176s CGAG 1176s CGAG 1176s Processing line... 1176s CGAG 1176s CGAG 1176s Processing line... 1176s CGAG 1176s CGAG 1176s Processing line... 1176s CTCG 1176s CTCG 1176s Processing line... 1176s CTCG 1176s CTCG 1176s Processing line... 1176s CGAG 1176s CGAG 1176s Processing line... 1176s CTCG 1176s CTCG 1176s Processing line... 1176s CGAG 1176s CGAG 1176s Processing line... 1176s CTCG 1176s CTCG 1176s Processing line... 1176s CGAG 1176s CGAG 1176s Processing line... 1176s CGAG 1176s CGAG 1176s Processing line... 1176s Processing line... 1176s GAGC 1176s GAGC 1176s Processing line... 1176s AGCCT 1176s AGCCT 1176s Processing line... 1176s GAGC 1176s GAGC 1176s Processing line... 1176s AGCCT 1176s AGCCT 1176s Processing line... 1176s GAGC 1176s GAGC 1176s Processing line... 1176s AGCCT 1176s AGCCT 1176s Processing line... 1176s GAGC 1176s GAGC 1176s Processing line... 1176s AGCCT 1176s AGCCT 1176s Processing line... 1176s GAGC 1176s GAGC 1176s Processing line... 1176s AGCCT 1176s AGCCT 1176s Processing line... 1176s GAGC 1176s GAGC 1176s Processing line... 1176s AGCCT 1176s AGCCT 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GTCACATCGAGATGGAC 1176s GTCACATCGAGATGGAC 1176s Processing line... 1176s GTCACATCGAGATGGAC 1176s GTCACATCGAGATGGAC 1176s Processing line... 1176s GTCACATCGAGATGGAC 1176s GTCACATCGAGATGGAC 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s ACCAC 1176s ACCAC 1176s Processing line... 1176s ACCAC 1176s ACCAC 1176s Processing line... 1176s ACCAC 1176s ACCAC 1176s Processing line... 1176s Processing line... 1176s GTCGAGG 1176s GTCGAGG 1176s Processing line... 1176s Processing line... 1176s TCGT 1176s TCGT 1176s Processing line... 1176s ACGA 1176s ACGA 1176s Processing line... 1176s ACGA 1176s ACGA 1176s Processing line... 1176s ACGA 1176s ACGA 1176s Processing line... 1176s TCGT 1176s TCGT 1176s Processing line... 1176s TCGT 1176s TCGT 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s ACGAGCCTGTCACATCGAG 1176s ACGAGCCTGTCACATCGAG 1176s Processing line... 1176s ACGAGCCTGTCACATCGAG 1176s ACGAGCCTGTCACATCGAG 1176s Processing line... 1176s ACGAGCCTGTCACATCGAG 1176s ACGAGCCTGTCACATCGAG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GGTGA 1176s GGTGA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s ACGAGCCTG 1176s ACGAGCCTG 1176s Processing line... 1176s ACGAGCCTG 1176s ACGAGCCTG 1176s Processing line... 1176s ACGAGCCTG 1176s ACGAGCCTG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GAACACGAGCCTG 1176s GAACACGAGCCTG 1176s Processing line... 1176s GAACACGAGCCTG 1176s GAACACGAGCCTG 1176s Processing line... 1176s GAACACGAGCCTG 1176s GAACACGAGCCTG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s ATGGACCA 1176s ATGGACCA 1176s Processing line... 1176s ATGGACCA 1176s ATGGACCA 1176s Processing line... 1176s ATGGACCA 1176s ATGGACCA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s AGGG 1176s AGGG 1176s Processing line... 1176s AGGG 1176s AGGG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s ACGAGCCTGTCACA 1176s ACGAGCCTGTCACA 1176s Processing line... 1176s ACGAGCCTGTCACA 1176s ACGAGCCTGTCACA 1176s Processing line... 1176s ACGAGCCTGTCACA 1176s ACGAGCCTGTCACA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GACCA 1176s GACCA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s TAGAACACGAGCCTGTCA 1176s TAGAACACGAGCCTGTCA 1176s Processing line... 1176s TAGAACACGAGCCTGTCA 1176s TAGAACACGAGCCTGTCA 1176s Processing line... 1176s TAGAACACGAGCCTGTCA 1176s TAGAACACGAGCCTGTCA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s ACACG 1176s ACACG 1176s Processing line... 1176s GAAC 1176s GAAC 1176s Processing line... 1176s ACACG 1176s ACACG 1176s Processing line... 1176s GAAC 1176s GAAC 1176s Processing line... 1176s ACACG 1176s ACACG 1176s Processing line... 1176s GAAC 1176s GAAC 1176s Processing line... 1176s ACACG 1176s ACACG 1176s Processing line... 1176s GAAC 1176s GAAC 1176s Processing line... 1176s ACACG 1176s ACACG 1176s Processing line... 1176s GAAC 1176s GAAC 1176s Processing line... 1176s ACACG 1176s ACACG 1176s Processing line... 1176s GAAC 1176s GAAC 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s GC 1176s GC 1176s Processing line... 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s TG 1176s TG 1176s Processing line... 1176s CA 1176s CA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s TC 1176s TC 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s GA 1176s GA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s ACATCGAGATG 1176s ACATCGAGATG 1176s Processing line... 1176s ACATCGAGATG 1176s ACATCGAGATG 1176s Processing line... 1176s ACATCGAGATG 1176s ACATCGAGATG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s CACATCGAGAT 1176s CACATCGAGAT 1176s Processing line... 1176s GAGCTCGCAG 1176s GAGCTCGCAG 1176s Processing line... 1176s CACATCGAGAT 1176s CACATCGAGAT 1176s Processing line... 1176s GAGCTCGCAG 1176s GAGCTCGCAG 1176s Processing line... 1176s CACATCGAGAT 1176s CACATCGAGAT 1176s Processing line... 1176s GAGCTCGCAG 1176s GAGCTCGCAG 1176s Processing line... 1176s ACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1176s ACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1176s Processing line... 1176s ACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1176s ACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1176s Processing line... 1176s ACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1176s ACGAGCCTGTCACATCGAGATGGACCACCTCGTG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s TGGAT 1176s TGGAT 1176s Processing line... 1176s TGGAT 1176s TGGAT 1176s Processing line... 1176s TGGAT 1176s TGGAT 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GAGA 1176s GAGA 1176s Processing line... 1176s GAGA 1176s GAGA 1176s Processing line... 1176s GAGA 1176s GAGA 1176s Processing line... 1176s GAGA 1176s GAGA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GAGGACC 1176s GAGGACC 1176s Processing line... 1176s Processing line... 1176s ACACGAGCCTGTCACAT 1176s ACACGAGCCTGTCACAT 1176s Processing line... 1176s ACACGAGCCTGTCACAT 1176s ACACGAGCCTGTCACAT 1176s Processing line... 1176s ACACGAGCCTGTCACAT 1176s ACACGAGCCTGTCACAT 1176s Processing line... 1176s ATTAGAGCT 1176s ATTAGAGCT 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s CCTGTCACATCG 1176s CCTGTCACATCG 1176s Processing line... 1176s TAGAACAC 1176s TAGAACAC 1176s Processing line... 1176s CCTGTCACATCG 1176s CCTGTCACATCG 1176s Processing line... 1176s TAGAACAC 1176s TAGAACAC 1176s Processing line... 1176s CCTGTCACATCG 1176s CCTGTCACATCG 1176s Processing line... 1176s TAGAACAC 1176s TAGAACAC 1176s Processing line... 1176s CCTGTCACATCG 1176s CCTGTCACATCG 1176s Processing line... 1176s TAGAACAC 1176s TAGAACAC 1176s Processing line... 1176s CCTGTCACATCG 1176s CCTGTCACATCG 1176s Processing line... 1176s TAGAACAC 1176s TAGAACAC 1176s Processing line... 1176s CCTGTCACATCG 1176s CCTGTCACATCG 1176s Processing line... 1176s TAGAACAC 1176s TAGAACAC 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s AGA 1176s AGA 1176s Processing line... 1176s AGA 1176s AGA 1176s Processing line... 1176s AGA 1176s AGA 1176s Processing line... 1176s AGA 1176s AGA 1176s Processing line... 1176s AGA 1176s AGA 1176s Processing line... 1176s AGA 1176s AGA 1176s Processing line... 1176s AGA 1176s AGA 1176s Processing line... 1176s AGA 1176s AGA 1176s Processing line... 1176s Processing line... 1176s AGTAGAACACGAGCCTGTCA 1176s AGTAGAACACGAGCCTGTCA 1176s Processing line... 1176s AGTAGAACACGAGCCTGTCA 1176s AGTAGAACACGAGCCTGTCA 1176s Processing line... 1176s AGTAGAACACGAGCCTGTCA 1176s AGTAGAACACGAGCCTGTCA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s ACGAGCCTGT 1176s ACGAGCCTGT 1176s Processing line... 1176s ACAC 1176s ACAC 1176s Processing line... 1176s ACGAGCCTGT 1176s ACGAGCCTGT 1176s Processing line... 1176s ACAC 1176s ACAC 1176s Processing line... 1176s ACGAGCCTGT 1176s ACGAGCCTGT 1176s Processing line... 1176s ACAC 1176s ACAC 1176s Processing line... 1176s GAGCTCGCAGCGC 1176s GAGCTCGCAGCGC 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s GGT 1176s GGT 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s GGT 1176s GGT 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s GGT 1176s GGT 1176s Processing line... 1176s GCGG 1176s GCGG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s GT 1176s GT 1176s Processing line... 1176s AC 1176s AC 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s TGGACCACCTC 1176s TGGACCACCTC 1176s Processing line... 1176s TGGACCACCTC 1176s TGGACCACCTC 1176s Processing line... 1176s TGGACCACCTC 1176s TGGACCACCTC 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s GTAG 1176s GTAG 1176s Processing line... 1176s GTAG 1176s GTAG 1176s Processing line... 1176s GTAG 1176s GTAG 1176s Processing line... 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s GGT 1176s GGT 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s GGT 1176s GGT 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s GGT 1176s GGT 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s ACC 1176s ACC 1176s Processing line... 1176s Processing line... 1176s ATTAGA 1176s ATTAGA 1176s Processing line... 1176s TCG 1176s TCG 1176s Processing line... 1176s ATTAGA 1176s ATTAGA 1176s Processing line... 1176s TCG 1176s TCG 1176s Processing line... 1176s ACGAG 1176s ACGAG 1176s Processing line... 1176s CTCGT 1176s CTCGT 1176s Processing line... 1176s CTCGT 1176s CTCGT 1176s Processing line... 1176s ACGAG 1176s ACGAG 1176s Processing line... 1176s CTCGT 1176s CTCGT 1176s Processing line... 1176s ACGAG 1176s ACGAG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s TCGAGATGGACC 1176s TCGAGATGGACC 1176s Processing line... 1176s TCGAGATGGACC 1176s TCGAGATGGACC 1176s Processing line... 1176s TCGAGATGGACC 1176s TCGAGATGGACC 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s TT 1176s TT 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s AA 1176s AA 1176s Processing line... 1176s Processing line... 1176s GTCA 1176s GTCA 1176s Processing line... 1176s GTCA 1176s GTCA 1176s Processing line... 1176s GTCA 1176s GTCA 1176s Processing line... 1176s Processing line... 1176s AAC 1176s AAC 1176s Processing line... 1176s AAC 1176s AAC 1176s Processing line... 1176s AAC 1176s AAC 1176s Processing line... 1176s AAC 1176s AAC 1176s Processing line... 1176s AAC 1176s AAC 1176s Processing line... 1176s AAC 1176s AAC 1176s Processing line... 1176s AAC 1176s AAC 1176s Processing line... 1176s AAC 1176s AAC 1176s Processing line... 1176s Processing line... 1176s AGAACACGAGCCTGTCACATCGA 1176s AGAACACGAGCCTGTCACATCGA 1176s Processing line... 1176s AGAACACGAGCCTGTCACATCGA 1176s AGAACACGAGCCTGTCACATCGA 1176s Processing line... 1176s AGAACACGAGCCTGTCACATCGA 1176s AGAACACGAGCCTGTCACATCGA 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s ACATCGAGATGGACCACCTCG 1176s ACATCGAGATGGACCACCTCG 1176s Processing line... 1176s ACATCGAGATGGACCACCTCG 1176s ACATCGAGATGGACCACCTCG 1176s Processing line... 1176s ACATCGAGATGGACCACCTCG 1176s ACATCGAGATGGACCACCTCG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s CCT 1176s CCT 1176s Processing line... 1176s AGG 1176s AGG 1176s Processing line... 1176s CCT 1176s CCT 1176s Processing line... 1176s CCT 1176s CCT 1176s Processing line... 1176s CCT 1176s CCT 1176s Processing line... 1176s CCT 1176s CCT 1176s Processing line... 1176s AGG 1176s AGG 1176s Processing line... 1176s CCT 1176s CCT 1176s Processing line... 1176s AGG 1176s AGG 1176s Processing line... 1176s Processing line... 1176s Processing line... 1176s --- Summary --- 1176s Read 1 reference strings 1176s Checked 411 alignments, 0 edits 1176s --------------- 1176s PASSED 1176s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1176s /usr/bin/bowtie2 -R 1 -D 33 --score-min L,4.31661143336071,9.00034418098128 --cp-ival 1 --cp-min 4 --large-index --ma 32.2894374931241 -a --mp 5.51515988576626,1.05013603310174 --rdg 44.1521308193594 -f -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1176s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1176s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #1 of read '52' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1176s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '13' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1176s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '62' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1176s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '15' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1176s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1176s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '28' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 1176s Warning: skipping mate #2 of read '126' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '126' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1176s Warning: skipping mate #2 of read '96' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '96' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1176s Warning: skipping mate #1 of read '102' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #1 of read '102' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1176s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '103' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 1176s Warning: skipping mate #2 of read '151' because length (1) <= # seed mismatches (0) 1176s Warning: skipping mate #2 of read '151' because it was < 2 characters long 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 1176s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 1177s 174 reads; of these: 1177s 174 (100.00%) were paired; of these: 1177s 167 (95.98%) aligned concordantly 0 times 1177s 0 (0.00%) aligned concordantly exactly 1 time 1177s 7 (4.02%) aligned concordantly >1 times 1177s ---- 1177s 167 pairs aligned concordantly 0 times; of these: 1177s 0 (0.00%) aligned discordantly 1 time 1177s ---- 1177s 167 pairs aligned 0 times concordantly or discordantly; of these: 1177s 334 mates make up the pairs; of these: 1177s 287 (85.93%) aligned 0 times 1177s 7 (2.10%) aligned exactly 1 time 1177s 40 (11.98%) aligned >1 times 1177s 17.53% overall alignment rate 1177s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1177s Flattened IUPAC characters 1177s Mutating sequence Sim.pm.1 1177s Introducing 5 SNPs, 2/0 ref/read gaps, and 1 rearrangements 1177s Finished SNPs 1177s Finished ref gaps 1177s Finished read gaps 1177s Mutating sequence Sim.pm.2 1177s Introducing 10 SNPs, 0/1 ref/read gaps, and 2 rearrangements 1177s Finished SNPs 1177s Finished ref gaps 1177s Finished read gaps 1177s Mutated reference genome to subject genome 1177s SNPs introduced: 15 1177s Reference gaps introduced: 2 1177s Read gaps introduced: 1 1177s Rearrangements introduced: 3 1177s Created read sampler 1177s Sampling 117 reads 1177s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1177s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1177s parsing sequence Sim.pm.1... 1177s parsing sequence Sim.pm.2... 1177s Parsed 269 reference bases 1177s *** Run 89 of 100 1177s /usr/bin/bowtie2 --cp-min 3 --mm --cp-ival 1 --rdg 15.0789652558565 -a --trim3 7 --large-index -R 1 -i S,2.86268010750777,1.01607646437665 --trim5 0 --gbar 3 --score-min L,5.54707863950249,6.80118536581321 --qseq -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.qseq -2 /tmp/Sim.pm.4OZZSEW9_2.qseq 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 1177s 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 1177s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Read 50 alignments... 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 1177s 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 1177s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Read 100 alignments... 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s Read 150 alignments... 1177s 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 1177s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #2 of read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 1177s Warning: skipping mate #2 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s Read 200 alignments... 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 1177s Read 250 alignments... 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 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 1177s 117 reads; of these: 1177s 102 (87.18%) were paired; of these: 1177s 101 (99.02%) aligned concordantly 0 times 1177s 0 (0.00%) aligned concordantly exactly 1 time 1177s 1 (0.98%) aligned concordantly >1 times 1177s ---- 1177s 101 pairs aligned concordantly 0 times; of these: 1177s 0 (0.00%) aligned discordantly 1 time 1177s ---- 1177s 101 pairs aligned 0 times concordantly or discordantly; of these: 1177s 202 mates make up the pairs; of these: 1177s 172 (85.15%) aligned 0 times 1177s 3 (1.49%) aligned exactly 1 time 1177s 27 (13.37%) aligned >1 times 1177s 15 (12.82%) were unpaired; of these: 1177s 12 (80.00%) aligned 0 times 1177s 0 (0.00%) aligned exactly 1 time 1177s 3 (20.00%) aligned >1 times 1177s 15.98% overall alignment rate 1177s Read 300 alignments... 1177s Read 350 alignments... 1177s Read 400 alignments... 1177s Read 450 alignments... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s TC 1177s TC 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s ACACGAGCCTGT 1177s ACACGAGCCTGT 1177s Processing line... 1177s ACACGAGCCTGT 1177s ACACGAGCCTGT 1177s Processing line... 1177s ACACGAGCCTGT 1177s ACACGAGCCTGT 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s AGATGGACCACCTCGTGGG 1177s AGATGGACCACCTCGTGGG 1177s Processing line... 1177s AGATGGACCACCTCGTGGG 1177s AGATGGACCACCTCGTGGG 1177s Processing line... 1177s AGATGGACCACCTCGTGGG 1177s AGATGGACCACCTCGTGGG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s ACCACC 1177s ACCACC 1177s Processing line... 1177s ACCACC 1177s ACCACC 1177s Processing line... 1177s ACCACC 1177s ACCACC 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s TAGAACACGAGCCTGTCACATCGAGATGG 1177s TAGAACACGAGCCTGTCACATCGAGATGG 1177s Processing line... 1177s TAGAACACGAGCCTGTCACATCGAGATGG 1177s TAGAACACGAGCCTGTCACATCGAGATGG 1177s Processing line... 1177s TAGAACACGAGCCTGTCACATCGAGATGG 1177s TAGAACACGAGCCTGTCACATCGAGATGG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GGG 1177s GGG 1177s Processing line... 1177s GGG 1177s GGG 1177s Processing line... 1177s GGG 1177s GGG 1177s Processing line... 1177s GGG 1177s GGG 1177s Processing line... 1177s GGG 1177s GGG 1177s Processing line... 1177s GGG 1177s GGG 1177s Processing line... 1177s GGG 1177s GGG 1177s Processing line... 1177s Processing line... 1177s GACCACCTCGTGGG 1177s GACCACCTCGTGGG 1177s Processing line... 1177s GACCACCTCGTGGG 1177s GACCACCTCGTGGG 1177s Processing line... 1177s GACCACCTCGTGGG 1177s GACCACCTCGTGGG 1177s Processing line... 1177s TATGGTGAGG 1177s TATGGTGAGG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s AGCTC 1177s AGCTC 1177s Processing line... 1177s GAGCT 1177s GAGCT 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s ACATCGAGATGGACCACCTCG 1177s ACATCGAGATGGACCACCTCG 1177s Processing line... 1177s ACATCGAGATGGACCACCTCG 1177s ACATCGAGATGGACCACCTCG 1177s Processing line... 1177s ACATCGAGATGGACCACCTCG 1177s ACATCGAGATGGACCACCTCG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GAGAT 1177s GAGAT 1177s Processing line... 1177s GAGAT 1177s GAGAT 1177s Processing line... 1177s GAGAT 1177s GAGAT 1177s Processing line... 1177s Processing line... 1177s AGG 1177s AGG 1177s Processing line... 1177s CCT 1177s CCT 1177s Processing line... 1177s AGG 1177s AGG 1177s Processing line... 1177s AGG 1177s AGG 1177s Processing line... 1177s CCT 1177s CCT 1177s Processing line... 1177s CCT 1177s CCT 1177s Processing line... 1177s CCT 1177s CCT 1177s Processing line... 1177s CCT 1177s CCT 1177s Processing line... 1177s CCT 1177s CCT 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s ACCA 1177s ACCA 1177s Processing line... 1177s ACCA 1177s ACCA 1177s Processing line... 1177s ACCA 1177s ACCA 1177s Processing line... 1177s ACCA 1177s ACCA 1177s Processing line... 1177s TGGT 1177s TGGT 1177s Processing line... 1177s ACCA 1177s ACCA 1177s Processing line... 1177s ACCA 1177s ACCA 1177s Processing line... 1177s ACCA 1177s ACCA 1177s Processing line... 1177s CTCGTGGG 1177s CTCGTGGG 1177s Processing line... 1177s CTCGTGGG 1177s CTCGTGGG 1177s Processing line... 1177s CTCGTGGG 1177s CTCGTGGG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s CAAA 1177s CAAA 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s CATCGAGATGGACCACCTCGT 1177s CATCGAGATGGACCACCTCGT 1177s Processing line... 1177s CATCGAGATGGACCACCTCGT 1177s CATCGAGATGGACCACCTCGT 1177s Processing line... 1177s CATCGAGATGGACCACCTCGT 1177s CATCGAGATGGACCACCTCGT 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s CTG 1177s CTG 1177s Processing line... 1177s CTG 1177s CTG 1177s Processing line... 1177s CTG 1177s CTG 1177s Processing line... 1177s CAG 1177s CAG 1177s Processing line... 1177s CTG 1177s CTG 1177s Processing line... 1177s CTG 1177s CTG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s CTGTCACATCG 1177s CTGTCACATCG 1177s Processing line... 1177s CTGTCACATCG 1177s CTGTCACATCG 1177s Processing line... 1177s CTGTCACATCG 1177s CTGTCACATCG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s AGCCTGTCACATCGA 1177s AGCCTGTCACATCGA 1177s Processing line... 1177s AGCCTGTCACATCGA 1177s AGCCTGTCACATCGA 1177s Processing line... 1177s AGCCTGTCACATCGA 1177s AGCCTGTCACATCGA 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GAT 1177s GAT 1177s Processing line... 1177s GAT 1177s GAT 1177s Processing line... 1177s GAT 1177s GAT 1177s Processing line... 1177s GAT 1177s GAT 1177s Processing line... 1177s GAT 1177s GAT 1177s Processing line... 1177s GAT 1177s GAT 1177s Processing line... 1177s ATC 1177s ATC 1177s Processing line... 1177s ATC 1177s ATC 1177s Processing line... 1177s ATC 1177s ATC 1177s Processing line... 1177s GAT 1177s GAT 1177s Processing line... 1177s GAT 1177s GAT 1177s Processing line... 1177s ATC 1177s ATC 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s CCTCGTG 1177s CCTCGTG 1177s Processing line... 1177s CCTCGTG 1177s CCTCGTG 1177s Processing line... 1177s CCTCGTG 1177s CCTCGTG 1177s Processing line... 1177s Processing line... 1177s TCACATCGAGATGGACCACCTCGTGG 1177s TCACATCGAGATGGACCACCTCGTGG 1177s Processing line... 1177s TCACATCGAGATGGACCACCTCGTGG 1177s TCACATCGAGATGGACCACCTCGTGG 1177s Processing line... 1177s TCACATCGAGATGGACCACCTCGTGG 1177s TCACATCGAGATGGACCACCTCGTGG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s AAT 1177s AAT 1177s Processing line... 1177s ATT 1177s ATT 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s TTAGA 1177s TTAGA 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GATGGACCACCTCG 1177s GATGGACCACCTCG 1177s Processing line... 1177s GATGGACCACCTCG 1177s GATGGACCACCTCG 1177s Processing line... 1177s GATGGACCACCTCG 1177s GATGGACCACCTCG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GAACACGAGCCTGTCACATCGAGATGGACCACCT 1177s GAACACGAGCCTGTCACATCGAGATGGACCACCT 1177s Processing line... 1177s GAACACGAGCCTGTCACATCGAGATGGACCACCT 1177s GAACACGAGCCTGTCACATCGAGATGGACCACCT 1177s Processing line... 1177s GAACACGAGCCTGTCACATCGAGATGGACCACCT 1177s GAACACGAGCCTGTCACATCGAGATGGACCACCT 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s GA 1177s GA 1177s Processing line... 1177s AGGGT 1177s AGGGT 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s ATT 1177s ATT 1177s Processing line... 1177s AAT 1177s AAT 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s GT 1177s GT 1177s Processing line... 1177s AC 1177s AC 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GAGCCT 1177s GAGCCT 1177s Processing line... 1177s GAGCCT 1177s GAGCCT 1177s Processing line... 1177s GAGCCT 1177s GAGCCT 1177s Processing line... 1177s ACGAG 1177s ACGAG 1177s Processing line... 1177s CTCGT 1177s CTCGT 1177s Processing line... 1177s CTCGT 1177s CTCGT 1177s Processing line... 1177s ACGAG 1177s ACGAG 1177s Processing line... 1177s CTCGT 1177s CTCGT 1177s Processing line... 1177s ACGAG 1177s ACGAG 1177s Processing line... 1177s Processing line... 1177s AGAACACGAGCCTGTCACATCG 1177s AGAACACGAGCCTGTCACATCG 1177s Processing line... 1177s AGAACACGAGCCTGTCACATCG 1177s AGAACACGAGCCTGTCACATCG 1177s Processing line... 1177s AGAACACGAGCCTGTCACATCG 1177s AGAACACGAGCCTGTCACATCG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s ACACGAG 1177s ACACGAG 1177s Processing line... 1177s ACACGAG 1177s ACACGAG 1177s Processing line... 1177s ACACGAG 1177s ACACGAG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s TG 1177s TG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s --- Summary --- 1177s Read 1 reference strings 1177s Checked 268 alignments, 0 edits 1177s --------------- 1177s PASSED 1177s Flattened IUPAC characters 1177s Mutating sequence Sim.pm.2 1177s Introducing 1 SNPs, 2/1 ref/read gaps, and 4 rearrangements 1177s Finished SNPs 1177s Finished ref gaps 1177s Finished read gaps 1177s Mutating sequence Sim.pm.1 1177s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1177s Finished SNPs 1177s Finished ref gaps 1177s Finished read gaps 1177s Mutated reference genome to subject genome 1177s SNPs introduced: 5 1177s Reference gaps introduced: 2 1177s Read gaps introduced: 1 1177s Rearrangements introduced: 4 1177s Created read sampler 1177s Sampling 68 reads 1177s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1177s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1177s parsing sequence Sim.pm.1... 1177s parsing sequence Sim.pm.2... 1177s *** Run 90 of 100 1177s /usr/bin/bowtie2 --cp-min 4 --nofw --mm --cp-ival 1 --trim5 6 --rdg 17.5183225763298 -a --n-ceil 0.0254757738045607,0.671710312178068 --large-index --score-min L,5.5099605616865,6.03845022258734 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1177s Parsed 269 reference bases 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1177s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1177s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1177s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1177s Warning: skipping read '10' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1177s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1177s Warning: skipping read '11' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1177s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1177s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1177s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 1177s Warning: skipping mate #2 of read '26' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1177s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1177s Warning: skipping read '33' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1177s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1177s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1177s Warning: skipping mate #2 of read '34' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1177s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1177s Warning: skipping read '40' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1177s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 1177s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1177s Read 50 alignments... 1177s Read 100 alignments... 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1177s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 1177s Warning: skipping mate #2 of read '58' because it was < 2 characters long 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1177s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1177s 68 reads; of these: 1177s 57 (83.82%) were paired; of these: 1177s 56 (98.25%) aligned concordantly 0 times 1177s 0 (0.00%) aligned concordantly exactly 1 time 1177s 1 (1.75%) aligned concordantly >1 times 1177s ---- 1177s 56 pairs aligned concordantly 0 times; of these: 1177s 0 (0.00%) aligned discordantly 1 time 1177s ---- 1177s 56 pairs aligned 0 times concordantly or discordantly; of these: 1177s 112 mates make up the pairs; of these: 1177s 103 (91.96%) aligned 0 times 1177s 2 (1.79%) aligned exactly 1 time 1177s 7 (6.25%) aligned >1 times 1177s 11 (16.18%) were unpaired; of these: 1177s 10 (90.91%) aligned 0 times 1177s 1 (9.09%) aligned exactly 1 time 1177s 0 (0.00%) aligned >1 times 1177s 9.60% overall alignment rate 1177s Read 150 alignments... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s ATA 1177s ATA 1177s Processing line... 1177s ATA 1177s ATA 1177s Processing line... 1177s ATA 1177s ATA 1177s Processing line... 1177s ATA 1177s ATA 1177s Processing line... 1177s ATA 1177s ATA 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GAA 1177s GAA 1177s Processing line... 1177s GAA 1177s GAA 1177s Processing line... 1177s GAA 1177s GAA 1177s Processing line... 1177s GAA 1177s GAA 1177s Processing line... 1177s GAA 1177s GAA 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GGATAACCAA 1177s GGATAACCAA 1177s Processing line... 1177s Processing line... 1177s GTCACATC 1177s GTCACATC 1177s Processing line... 1177s GTCACATC 1177s GTCACATC 1177s Processing line... 1177s GTCACATC 1177s GTCACATC 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s GTCGAGGACC 1177s GTCGAGGACC 1177s Processing line... 1177s GATA 1177s GATA 1177s Processing line... 1177s GTCGAGGACC 1177s GTCGAGGACC 1177s Processing line... 1177s GATA 1177s GATA 1177s Processing line... 1177s GTCGAGGACC 1177s GTCGAGGACC 1177s Processing line... 1177s GATA 1177s GATA 1177s Processing line... 1177s GTCGAGGACC 1177s GTCGAGGACC 1177s Processing line... 1177s GATA 1177s GATA 1177s Processing line... 1177s AGGGTCGAGGA 1177s AGGGTCGAGGA 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s CG 1177s CG 1177s Processing line... 1177s Processing line... 1177s TATG 1177s TATG 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s Processing line... 1177s TAGAACACGAGCCTGTC 1177s TAGAACACGAGCCTGTC 1177s Processing line... 1177s TAGAACACGAGCCTGTC 1177s TAGAACACGAGCCTGTC 1177s Processing line... 1177s TAGAACACGAGCCTGTC 1177s TAGAACACGAGCCTGTC 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s CA 1177s CA 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s Processing line... 1177s --- Summary --- 1177s Read 1 reference strings 1177s Checked 77 alignments, 0 edits 1177s --------------- 1177s PASSED 1177s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1177s /usr/bin/bowtie2 --cp-min 4 --nofw --mm --cp-ival 1 --trim5 6 --rdg 17.5183225763298 -a --n-ceil 0.0254757738045607,0.671710312178068 --large-index --score-min L,5.5099605616865,6.03845022258734 -f -p 2 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1178s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1178s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1178s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1178s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1178s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read '10' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1178s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read '11' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1178s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 1178s Warning: skipping mate #2 of read '26' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1178s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read '33' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1178s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1178s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1178s Warning: skipping mate #2 of read '34' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1178s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read '40' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1178s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1178s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 1178s Warning: skipping mate #2 of read '58' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1178s 68 reads; of these: 1178s 57 (83.82%) were paired; of these: 1178s 56 (98.25%) aligned concordantly 0 times 1178s 0 (0.00%) aligned concordantly exactly 1 time 1178s 1 (1.75%) aligned concordantly >1 times 1178s ---- 1178s 56 pairs aligned concordantly 0 times; of these: 1178s 0 (0.00%) aligned discordantly 1 time 1178s ---- 1178s 56 pairs aligned 0 times concordantly or discordantly; of these: 1178s 112 mates make up the pairs; of these: 1178s 103 (91.96%) aligned 0 times 1178s 2 (1.79%) aligned exactly 1 time 1178s 7 (6.25%) aligned >1 times 1178s 11 (16.18%) were unpaired; of these: 1178s 10 (90.91%) aligned 0 times 1178s 1 (9.09%) aligned exactly 1 time 1178s 0 (0.00%) aligned >1 times 1178s 9.60% overall alignment rate 1178s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1178s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1178s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1178s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1178s /usr/bin/bowtie2 --cp-min 4 --nofw --mm --cp-ival 1 --trim5 6 --rdg 17.5183225763298 -a --n-ceil 0.0254757738045607,0.671710312178068 --large-index --score-min L,5.5099605616865,6.03845022258734 -f -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1178s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '2' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1178s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '5' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1178s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1178s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1178s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read '33' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1178s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1178s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1178s Warning: skipping mate #2 of read '34' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1178s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read '10' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1178s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read '11' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1178s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 1178s Warning: skipping mate #2 of read '26' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1178s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read '40' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1178s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 1178s Warning: skipping mate #1 of read '46' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1178s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 1178s Warning: skipping mate #2 of read '58' because it was < 2 characters long 1178s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1178s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1178s 68 reads; of these: 1178s 57 (83.82%) were paired; of these: 1178s 56 (98.25%) aligned concordantly 0 times 1178s 0 (0.00%) aligned concordantly exactly 1 time 1178s 1 (1.75%) aligned concordantly >1 times 1178s ---- 1178s 56 pairs aligned concordantly 0 times; of these: 1178s 0 (0.00%) aligned discordantly 1 time 1178s ---- 1178s 56 pairs aligned 0 times concordantly or discordantly; of these: 1178s 112 mates make up the pairs; of these: 1178s 103 (91.96%) aligned 0 times 1178s 2 (1.79%) aligned exactly 1 time 1178s 7 (6.25%) aligned >1 times 1178s 11 (16.18%) were unpaired; of these: 1178s 10 (90.91%) aligned 0 times 1178s 1 (9.09%) aligned exactly 1 time 1178s 0 (0.00%) aligned >1 times 1178s 9.60% overall alignment rate 1178s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1178s Flattened IUPAC characters 1178s Mutating sequence Sim.pm.1 1178s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1178s Finished SNPs 1178s Finished ref gaps 1178s Finished read gaps 1178s Mutating sequence Sim.pm.2 1178s Introducing 20 SNPs, 5/0 ref/read gaps, and 0 rearrangements 1178s Finished SNPs 1178s Finished ref gaps 1178s Finished read gaps 1178s Mutated reference genome to subject genome 1178s SNPs introduced: 22 1178s Reference gaps introduced: 5 1178s Read gaps introduced: 0 1178s Rearrangements introduced: 0 1178s Created read sampler 1178s Sampling 97 reads 1178s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.qseq & /tmp/Sim.pm.4OZZSEW9_2.qseq 1178s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1178s parsing sequence Sim.pm.1... 1178s parsing sequence Sim.pm.2... 1178s Parsed 269 reference bases 1178s *** Run 91 of 100 1178s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 4 --ma 20.2577111948773 --large-index --trim3 3 -a --np 2 --score-min L,2.05163588346404,4.28775268209119 --qseq -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.qseq 1178s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s Read 50 alignments... 1178s Read 100 alignments... 1178s 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 1178s 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 1178s 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 1178s 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 1178s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (1) <= # seed mismatches (0) 1178s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1178s 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 1178s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1178s 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 1178s 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 1178s Read 150 alignments... 1178s Read 200 alignments... 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 1178s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 1178s 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 1178s 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 1178s 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 1178s 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 1178s 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 1178s Read 250 alignments... 1178s 97 reads; of these: 1178s 97 (100.00%) were unpaired; of these: 1178s 76 (78.35%) aligned 0 times 1178s 4 (4.12%) aligned exactly 1 time 1178s 17 (17.53%) aligned >1 times 1178s 21.65% overall alignment rate 1178s Read 300 alignments... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s TGAAGTGGCTGA 1178s TGAAGTGGCTGA 1178s Processing line... 1178s TGAAGTGGCTGA 1178s TGAAGTGGCTGA 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s CC 1178s CC 1178s Processing line... 1178s GG 1178s GG 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s AT 1178s AT 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s CTGA 1178s CTGA 1178s Processing line... 1178s CTGA 1178s CTGA 1178s Processing line... 1178s CTG 1178s CTG 1178s Processing line... 1178s CAG 1178s CAG 1178s Processing line... 1178s CTG 1178s CTG 1178s Processing line... 1178s CTG 1178s CTG 1178s Processing line... 1178s CTG 1178s CTG 1178s Processing line... 1178s CTG 1178s CTG 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s TA 1178s TA 1178s Processing line... 1178s AACC 1178s AACC 1178s Processing line... 1178s AACC 1178s AACC 1178s Processing line... 1178s AACC 1178s AACC 1178s Processing line... 1178s AACC 1178s AACC 1178s Processing line... 1178s CCACC 1178s CCACC 1178s Processing line... 1178s CCACC 1178s CCACC 1178s Processing line... 1178s CCACC 1178s CCACC 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s AACC 1178s AACC 1178s Processing line... 1178s AACC 1178s AACC 1178s Processing line... 1178s AACC 1178s AACC 1178s Processing line... 1178s AACC 1178s AACC 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s TGAAGTGGCTGA 1178s TGAAGTGGCTGA 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s GCTGAA 1178s GCTGAA 1178s Processing line... 1178s AGG 1178s AGG 1178s Processing line... 1178s CCT 1178s CCT 1178s Processing line... 1178s CCT 1178s CCT 1178s Processing line... 1178s CCT 1178s CCT 1178s Processing line... 1178s CCT 1178s CCT 1178s Processing line... 1178s AGG 1178s AGG 1178s Processing line... 1178s CCT 1178s CCT 1178s Processing line... 1178s AGG 1178s AGG 1178s Processing line... 1178s CCT 1178s CCT 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s TG 1178s TG 1178s Processing line... 1178s CA 1178s CA 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s ACACGAGCCTGTCACAT 1178s ACACGAGCCTGTCACAT 1178s Processing line... 1178s ACACGAGCCTGTCACAT 1178s ACACGAGCCTGTCACAT 1178s Processing line... 1178s ACACGAGCCTGTCACAT 1178s ACACGAGCCTGTCACAT 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s GAG 1178s GAG 1178s Processing line... 1178s GAG 1178s GAG 1178s Processing line... 1178s GAG 1178s GAG 1178s Processing line... 1178s CTC 1178s CTC 1178s Processing line... 1178s GAG 1178s GAG 1178s Processing line... 1178s CTC 1178s CTC 1178s Processing line... 1178s GAG 1178s GAG 1178s Processing line... 1178s CTC 1178s CTC 1178s Processing line... 1178s GAG 1178s GAG 1178s Processing line... 1178s GAG 1178s GAG 1178s Processing line... 1178s GAG 1178s GAG 1178s Processing line... 1178s GAG 1178s GAG 1178s Processing line... 1178s GAG 1178s GAG 1178s Processing line... 1178s CTC 1178s CTC 1178s Processing line... 1178s Processing line... 1178s AGAT 1178s AGAT 1178s Processing line... 1178s AGAT 1178s AGAT 1178s Processing line... 1178s AGAT 1178s AGAT 1178s Processing line... 1178s Processing line... 1178s Processing line... 1178s TGGACCAC 1178s TGGACCAC 1178s Processing line... 1178s TGGACCAC 1178s TGGACCAC 1178s Processing line... 1178s TGGACCAC 1178s TGGACCAC 1178s Processing line... 1178s TCACAT 1178s TCACAT 1178s Processing line... 1178s TCACAT 1178s TCACAT 1178s Processing line... 1178s TCACAT 1178s TCACAT 1178s Processing line... 1178s Processing line... 1178s --- Summary --- 1178s Read 1 reference strings 1178s Checked 254 alignments, 0 edits 1178s --------------- 1178s PASSED 1178s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1178s /usr/bin/bowtie2 --cp-ival 1 --mm --cp-min 4 --ma 20.2577111948773 --large-index --trim3 3 -a --np 2 --score-min L,2.05163588346404,4.28775268209119 --qseq -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1179s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1179s *** Run 92 of 100 1179s /usr/bin/bowtie2 --cp-ival 2 --cp-min 2 --large-index --rdg 15.9805933997736,3.42680299295031 --trim3 3 --mp 6.72303549826984,3.00044555451622 -D 39 -R 1 -N 0 -L19 --np 3 --score-min L,3.82971054386599,1.35329206102985 --n-ceil 0.423775278041558,0.594084759241531 --rfg 15.417277033659,16.9395331236815 -q -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq 1179s 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 1179s 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 1179s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 1179s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 1179s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (1) <= # seed mismatches (0) 1179s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 1179s 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 1179s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 1179s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s 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 1179s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 1179s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 1179s 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 1179s 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 1179s 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 1179s 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 1179s 97 reads; of these: 1179s 97 (100.00%) were unpaired; of these: 1179s 76 (78.35%) aligned 0 times 1179s 4 (4.12%) aligned exactly 1 time 1179s 17 (17.53%) aligned >1 times 1179s 21.65% overall alignment rate 1179s Flattened IUPAC characters 1179s Mutating sequence Sim.pm.1 1179s Introducing 5 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1179s Finished SNPs 1179s Finished ref gaps 1179s Finished read gaps 1179s Mutating sequence Sim.pm.2 1179s Introducing 6 SNPs, 2/1 ref/read gaps, and 1 rearrangements 1179s Finished SNPs 1179s Finished ref gaps 1179s Finished read gaps 1179s Mutated reference genome to subject genome 1179s SNPs introduced: 11 1179s Reference gaps introduced: 2 1179s Read gaps introduced: 1 1179s Rearrangements introduced: 3 1179s Created read sampler 1179s Sampling 51 reads 1179s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1179s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1179s parsing sequence Sim.pm.1... 1179s parsing sequence Sim.pm.2... 1179s Parsed 269 reference bases 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1179s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 1179s Warning: skipping mate #2 of read '7' because it was < 2 characters long 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1179s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1179s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1179s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 1179s Warning: skipping mate #1 of read '31' because it was < 2 characters long 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1179s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 1179s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1179s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1179s Warning: skipping read '49' because it was < 2 characters long 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1179s 51 reads; of these: 1179s 42 (82.35%) were paired; of these: 1179s 40 (95.24%) aligned concordantly 0 times 1179s 0 (0.00%) aligned concordantly exactly 1 time 1179s 2 (4.76%) aligned concordantly >1 times 1179s ---- 1179s 40 pairs aligned concordantly 0 times; of these: 1179s 0 (0.00%) aligned discordantly 1 time 1179s ---- 1179s 40 pairs aligned 0 times concordantly or discordantly; of these: 1179s 80 mates make up the pairs; of these: 1179s 65 (81.25%) aligned 0 times 1179s 1 (1.25%) aligned exactly 1 time 1179s 14 (17.50%) aligned >1 times 1179s 9 (17.65%) were unpaired; of these: 1179s 7 (77.78%) aligned 0 times 1179s 0 (0.00%) aligned exactly 1 time 1179s 2 (22.22%) aligned >1 times 1179s 22.58% overall alignment rate 1179s Read 50 alignments... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s ACCACCT 1179s ACCACCT 1179s Processing line... 1179s GA 1179s GA 1179s Processing line... 1179s TAACCAAAACGC 1179s TAACCAAAACGC 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s CATCGAGAT 1179s CATCGAGAT 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s AGATGG 1179s AGATGG 1179s Processing line... 1179s Processing line... 1179s AACACGAGCCTGTCACATCGAGATG 1179s AACACGAGCCTGTCACATCGAGATG 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s TGTCACATCGAG 1179s TGTCACATCGAG 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s GTCACATCGAGATGGACCACCTCG 1179s GTCACATCGAGATGGACCACCTCG 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s CGA 1179s CGA 1179s Processing line... 1179s CGAGCC 1179s CGAGCC 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s AGCCTGTCACATCGAGATGGACCACCTCG 1179s AGCCTGTCACATCGAGATGGACCACCTCG 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s CGAGATGG 1179s CGAGATGG 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s GAACACGAGCCTGTCACATCG 1179s GAACACGAGCCTGTCACATCG 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s ATGGACCACC 1179s ATGGACCACC 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s GAACACGAGCCTGTC 1179s GAACACGAGCCTGTC 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s AGCCTGTCACATCG 1179s AGCCTGTCACATCG 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s CACG 1179s CACG 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s GAGG 1179s GAGG 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s CCTGTCACATCGA 1179s CCTGTCACATCGA 1179s Processing line... 1179s Processing line... 1179s TGGTG 1179s TGGTG 1179s Processing line... 1179s Processing line... 1179s GAGA 1179s GAGA 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s Processing line... 1179s --- Summary --- 1179s Read 1 reference strings 1179s Checked 21 alignments, 0 edits 1179s /usr/bin/bowtie2 --cp-ival 2 --cp-min 2 --large-index --rdg 15.9805933997736,3.42680299295031 --trim3 3 --mp 6.72303549826984,3.00044555451622 -D 39 -R 1 -N 0 -L19 --np 3 --score-min L,3.82971054386599,1.35329206102985 --n-ceil 0.423775278041558,0.594084759241531 --rfg 15.417277033659,16.9395331236815 -q -p 2 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fastq -2 /tmp/Sim.pm.4OZZSEW9_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1179s --------------- 1179s PASSED 1179s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1179s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 1179s Warning: skipping mate #2 of read '7' because it was < 2 characters long 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1179s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 1179s Warning: skipping mate #1 of read '44' because it was < 2 characters long 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1179s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 1179s Warning: skipping mate #1 of read '28' because it was < 2 characters long 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1179s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 1179s Warning: skipping mate #1 of read '31' because it was < 2 characters long 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1179s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1179s Warning: skipping read '49' because it was < 2 characters long 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1179s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1179s 51 reads; of these: 1179s 42 (82.35%) were paired; of these: 1179s 40 (95.24%) aligned concordantly 0 times 1179s 0 (0.00%) aligned concordantly exactly 1 time 1179s 2 (4.76%) aligned concordantly >1 times 1179s ---- 1179s 40 pairs aligned concordantly 0 times; of these: 1179s 0 (0.00%) aligned discordantly 1 time 1179s ---- 1179s 40 pairs aligned 0 times concordantly or discordantly; of these: 1179s 80 mates make up the pairs; of these: 1179s 65 (81.25%) aligned 0 times 1179s 1 (1.25%) aligned exactly 1 time 1179s 14 (17.50%) aligned >1 times 1179s 9 (17.65%) were unpaired; of these: 1179s 7 (77.78%) aligned 0 times 1179s 0 (0.00%) aligned exactly 1 time 1179s 2 (22.22%) aligned >1 times 1179s 22.58% overall alignment rate 1179s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1179s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1179s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1179s Flattened IUPAC characters 1179s Mutating sequence Sim.pm.1 1179s Introducing 0 SNPs, 1/0 ref/read gaps, and 2 rearrangements 1179s Finished SNPs 1179s Finished ref gaps 1179s Finished read gaps 1179s Mutating sequence Sim.pm.2 1179s Introducing 24 SNPs, 1/4 ref/read gaps, and 1 rearrangements 1179s Finished SNPs 1179s Finished ref gaps 1179s Finished read gaps 1179s Mutated reference genome to subject genome 1179s SNPs introduced: 24 1179s Reference gaps introduced: 2 1179s Read gaps introduced: 4 1179s Rearrangements introduced: 3 1179s Created read sampler 1179s Sampling 79 reads 1179s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1179s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1179s parsing sequence Sim.pm.1... 1179s parsing sequence Sim.pm.2... 1179s Parsed 269 reference bases 1179s *** Run 93 of 100 1179s /usr/bin/bowtie2 --cp-ival 2 --mm --cp-min 2 --large-index --mp 4.25686510784251,4.11676619664073 -a --trim3 5 -D 32 -N 0 -L16 --np 1 --norc --score-min L,3.86424459398761,3.57505219703514 --trim5 5 -f -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.fasta -2 /tmp/Sim.pm.4OZZSEW9_2.fasta 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1180s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 1180s Warning: skipping read '1' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1180s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '3' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1180s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 1180s Warning: skipping mate #2 of read '8' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1180s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1180s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 1180s Warning: skipping read '12' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1180s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '18' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1180s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '20' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1180s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '21' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1180s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '22' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1180s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '25' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1180s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 1180s Warning: skipping mate #2 of read '36' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1180s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '38' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1180s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 1180s Warning: skipping read '40' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1180s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 1180s Warning: skipping read '49' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1180s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '58' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1180s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '63' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1180s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '65' because it was < 2 characters long 1180s Read 50 alignments... 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1180s Read 100 alignments... 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1180s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (0) 1180s Warning: skipping mate #1 of read '78' because it was < 2 characters long 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1180s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1180s 79 reads; of these: 1180s 65 (82.28%) were paired; of these: 1180s 65 (100.00%) aligned concordantly 0 times 1180s 0 (0.00%) aligned concordantly exactly 1 time 1180s 0 (0.00%) aligned concordantly >1 times 1180s ---- 1180s 65 pairs aligned concordantly 0 times; of these: 1180s 0 (0.00%) aligned discordantly 1 time 1180s ---- 1180s 65 pairs aligned 0 times concordantly or discordantly; of these: 1180s 130 mates make up the pairs; of these: 1180s 117 (90.00%) aligned 0 times 1180s 1 (0.77%) aligned exactly 1 time 1180s 12 (9.23%) aligned >1 times 1180s 14 (17.72%) were unpaired; of these: 1180s 13 (92.86%) aligned 0 times 1180s 0 (0.00%) aligned exactly 1 time 1180s 1 (7.14%) aligned >1 times 1180s 9.72% overall alignment rate 1180s Read 150 alignments... 1180s Read 200 alignments... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s AT 1180s AT 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s TGGACCACCTCG 1180s TGGACCACCTCG 1180s Processing line... 1180s TGGACCACCTCG 1180s TGGACCACCTCG 1180s Processing line... 1180s TGGACCACCTCG 1180s TGGACCACCTCG 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s AACACGAGCCTGTCA 1180s AACACGAGCCTGTCA 1180s Processing line... 1180s AACACGAGCCTGTCA 1180s AACACGAGCCTGTCA 1180s Processing line... 1180s AACACGAGCCTGTCA 1180s AACACGAGCCTGTCA 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s TCGAG 1180s TCGAG 1180s Processing line... 1180s TCGAG 1180s TCGAG 1180s Processing line... 1180s TCGAG 1180s TCGAG 1180s Processing line... 1180s TCGAG 1180s TCGAG 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s GGT 1180s GGT 1180s Processing line... 1180s GGT 1180s GGT 1180s Processing line... 1180s GGT 1180s GGT 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s ATAA 1180s ATAA 1180s Processing line... 1180s ATAA 1180s ATAA 1180s Processing line... 1180s ATAA 1180s ATAA 1180s Processing line... 1180s ATAA 1180s ATAA 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s ATGG 1180s ATGG 1180s Processing line... 1180s ATGG 1180s ATGG 1180s Processing line... 1180s ATGG 1180s ATGG 1180s Processing line... 1180s ATGG 1180s ATGG 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s GATGGACCACCTC 1180s GATGGACCACCTC 1180s Processing line... 1180s GATGGACCACCTC 1180s GATGGACCACCTC 1180s Processing line... 1180s GATGGACCACCTC 1180s GATGGACCACCTC 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s AGTAGAACACGAGC 1180s AGTAGAACACGAGC 1180s Processing line... 1180s AGTAGAACACGAGC 1180s AGTAGAACACGAGC 1180s Processing line... 1180s AGTAGAACACGAGC 1180s AGTAGAACACGAGC 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s CA 1180s CA 1180s Processing line... 1180s Processing line... 1180s GTGA 1180s GTGA 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s GCCT 1180s GCCT 1180s Processing line... 1180s GCCT 1180s GCCT 1180s Processing line... 1180s GCCT 1180s GCCT 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s AGTAGAA 1180s AGTAGAA 1180s Processing line... 1180s AGTAGAA 1180s AGTAGAA 1180s Processing line... 1180s AGTAGAA 1180s AGTAGAA 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s AACACGAGCCTGT 1180s AACACGAGCCTGT 1180s Processing line... 1180s AACACGAGCCTGT 1180s AACACGAGCCTGT 1180s Processing line... 1180s AACACGAGCCTGT 1180s AACACGAGCCTGT 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s --- Summary --- 1180s Read 1 reference strings 1180s Checked 68 alignments, 0 edits 1180s --------------- 1180s PASSED 1180s Flattened IUPAC characters 1180s Mutating sequence Sim.pm.2 1180s Introducing 0 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1180s Finished SNPs 1180s Finished ref gaps 1180s Finished read gaps 1180s Mutating sequence Sim.pm.1 1180s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1180s Finished SNPs 1180s Finished ref gaps 1180s Finished read gaps 1180s Mutated reference genome to subject genome 1180s SNPs introduced: 7 1180s Reference gaps introduced: 0 1180s Read gaps introduced: 0 1180s Rearrangements introduced: 3 1180s Created read sampler 1180s Sampling 62 reads 1180s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1180s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1180s parsing sequence Sim.pm.1... 1180s parsing sequence Sim.pm.2... 1180s Parsed 269 reference bases 1180s *** Run 94 of 100 1180s /usr/bin/bowtie2 --np 8 -D 24 -i S,1.78335500954891 --score-min L,4.12329074157389,9.34782894075171 --cp-min 7 --cp-ival 1 --mm --local --trim3 0 --mp 5.82802561967735,3.84919809651647 --large-index -r -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw 1180s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1180s Warning: skipping read '10' because it was < 2 characters long 1180s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 1180s Warning: skipping read '53' because it was < 2 characters long 1180s 62 reads; of these: 1180s 62 (100.00%) were unpaired; of these: 1180s 62 (100.00%) aligned 0 times 1180s 0 (0.00%) aligned exactly 1 time 1180s 0 (0.00%) aligned >1 times 1180s 0.00% overall alignment rate 1180s Read 50 alignments... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s Processing line... 1180s --- Summary --- 1180s Read 1 reference strings 1180s Checked 0 alignments, 0 edits 1180s --------------- 1180s PASSED 1180s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1180s /usr/bin/bowtie2 --np 8 -D 24 -i S,1.78335500954891 --score-min L,4.12329074157389,9.34782894075171 --cp-min 7 --cp-ival 1 --mm --local --trim3 0 --mp 5.82802561967735,3.84919809651647 --large-index -r -p 2 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1180s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 1180s Warning: skipping read '10' because it was < 2 characters long 1180s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 1180s Warning: skipping read '53' because it was < 2 characters long 1180s 62 reads; of these: 1180s 62 (100.00%) were unpaired; of these: 1180s 62 (100.00%) aligned 0 times 1180s 0 (0.00%) aligned exactly 1 time 1180s 0 (0.00%) aligned >1 times 1180s 0.00% overall alignment rate 1180s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1180s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1180s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1180s Flattened IUPAC characters 1180s Mutating sequence Sim.pm.1 1180s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1180s Finished SNPs 1180s Finished ref gaps 1180s Finished read gaps 1180s Mutating sequence Sim.pm.2 1180s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1180s Finished SNPs 1180s Finished ref gaps 1180s Finished read gaps 1180s Mutated reference genome to subject genome 1180s SNPs introduced: 8 1180s Reference gaps introduced: 0 1180s Read gaps introduced: 0 1180s Rearrangements introduced: 0 1180s Created read sampler 1180s Sampling 206 reads 1180s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fastq & /tmp/Sim.pm.4OZZSEW9_2.fastq 1180s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1180s parsing sequence Sim.pm.1... 1180s *** Run 95 of 100 1180s /usr/bin/bowtie2 --local --large-index --score-min L,7.82603853624932,9.05904441141467 --cp-min 5 --cp-ival 2 -R 4 --mm -q -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq 1180s parsing sequence Sim.pm.2... 1180s Parsed 269 reference bases 1180s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 1180s Warning: skipping read '13' because it was < 2 characters long 1180s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 1180s Warning: skipping read '14' because it was < 2 characters long 1180s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 1180s Warning: skipping read '46' because it was < 2 characters long 1180s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 1180s Warning: skipping read '58' because it was < 2 characters long 1180s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 1180s Warning: skipping read '74' because it was < 2 characters long 1180s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 1180s Warning: skipping read '96' because it was < 2 characters long 1180s Read 50 alignments... 1180s 206 reads; of these: 1180s 206 (100.00%) were unpaired; of these: 1180s 206 (100.00%) aligned 0 times 1180s 0 (0.00%) aligned exactly 1 time 1180s 0 (0.00%) aligned >1 times 1180s 0.00% overall alignment rate 1180s Read 100 alignments... 1180s Read 150 alignments... 1180s Read 200 alignments... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s --- Summary --- 1181s /usr/bin/bowtie2 --local --large-index --score-min L,7.82603853624932,9.05904441141467 --cp-min 5 --cp-ival 2 -R 4 --mm -q -p 3 -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1181s Read 1 reference strings 1181s Checked 0 alignments, 0 edits 1181s --------------- 1181s PASSED 1181s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1181s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 1181s Warning: skipping read '13' because it was < 2 characters long 1181s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 1181s Warning: skipping read '14' because it was < 2 characters long 1181s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 1181s Warning: skipping read '58' because it was < 2 characters long 1181s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 1181s Warning: skipping read '74' because it was < 2 characters long 1181s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 1181s Warning: skipping read '46' because it was < 2 characters long 1181s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 1181s Warning: skipping read '96' because it was < 2 characters long 1181s 206 reads; of these: 1181s 206 (100.00%) were unpaired; of these: 1181s 206 (100.00%) aligned 0 times 1181s 0 (0.00%) aligned exactly 1 time 1181s 0 (0.00%) aligned >1 times 1181s 0.00% overall alignment rate 1181s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1181s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1181s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1181s Flattened IUPAC characters 1181s Mutating sequence Sim.pm.1 1181s Introducing 12 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1181s Finished SNPs 1181s Finished ref gaps 1181s Finished read gaps 1181s Mutating sequence Sim.pm.2 1181s Introducing 25 SNPs, 5/1 ref/read gaps, and 0 rearrangements 1181s Finished SNPs 1181s Finished ref gaps 1181s Finished read gaps 1181s Mutated reference genome to subject genome 1181s SNPs introduced: 37 1181s Reference gaps introduced: 5 1181s Read gaps introduced: 1 1181s Rearrangements introduced: 0 1181s Created read sampler 1181s Sampling 11 reads 1181s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1181s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1181s parsing sequence Sim.pm.1... 1181s *** Run 96 of 100 1181s /usr/bin/bowtie2 --rfg 5.61811487960618,11.9445467858047 --score-min L,9.2753593886297,6.21784030390737 --large-index --ma 10.1441455405449 --cp-min 3 --mm --cp-ival 1 -D 3 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1181s parsing sequence Sim.pm.2... 1181s Parsed 269 reference bases 1181s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1181s 11 reads; of these: 1181s 11 (100.00%) were unpaired; of these: 1181s 8 (72.73%) aligned 0 times 1181s 0 (0.00%) aligned exactly 1 time 1181s 3 (27.27%) aligned >1 times 1181s 27.27% overall alignment rate 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s GAG 1181s GAG 1181s Processing line... 1181s Processing line... 1181s Processing line... 1181s TCACATCGA 1181s TCACATCGA 1181s Processing line... 1181s Processing line... 1181s ATGG 1181s ATGG 1181s --- Summary --- 1181s Read 1 reference strings 1181s Checked 3 alignments, 0 edits 1181s --------------- 1181s PASSED 1181s ALSO checking that bowtie2 and bowtie2-align match up 1181s /usr/bin/bowtie2 --rfg 5.61811487960618,11.9445467858047 --score-min L,9.2753593886297,6.21784030390737 --large-index --ma 10.1441455405449 --cp-min 3 --mm --cp-ival 1 -D 3 -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1181s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1181s 11 reads; of these: 1181s 11 (100.00%) were unpaired; of these: 1181s 8 (72.73%) aligned 0 times 1181s 0 (0.00%) aligned exactly 1 time 1181s 3 (27.27%) aligned >1 times 1181s 27.27% overall alignment rate 1181s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1181s Flattened IUPAC characters 1181s Mutating sequence Sim.pm.2 1181s Introducing 35 SNPs, 2/2 ref/read gaps, and 1 rearrangements 1181s Finished SNPs 1181s Finished ref gaps 1181s Finished read gaps 1181s Mutating sequence Sim.pm.1 1181s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 1181s Finished SNPs 1181s Finished ref gaps 1181s Finished read gaps 1181s Mutated reference genome to subject genome 1181s SNPs introduced: 37 1181s Reference gaps introduced: 2 1181s Read gaps introduced: 2 1181s Rearrangements introduced: 1 1181s Created read sampler 1181s Sampling 130 reads 1181s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1181s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1181s parsing sequence Sim.pm.1... 1181s parsing sequence Sim.pm.2... 1181s Parsed 269 reference bases 1181s *** Run 97 of 100 1181s /usr/bin/bowtie2 --cp-min 4 --cp-ival 2 --mm --mp 8.86827001618359,5.35071818754591 --large-index -k 4 --np 3 --norc --trim5 6 --n-ceil 0.361332891608261,1.1444179805813 --score-min L,6.06341886538575,4.29188284408769 --gbar 1 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1181s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1181s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1181s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 1181s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1181s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1181s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1181s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 1181s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1181s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1181s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1181s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 1181s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1181s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1181s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1181s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1181s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1181s Read 50 alignments... 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1181s Read 100 alignments... 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1181s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1182s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1182s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1182s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 1182s Warning: skipping mate #2 of read '97' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1182s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '111' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1182s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1182s Warning: skipping mate #1 of read '117' because length (1) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '117' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1182s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '119' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1182s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 1182s Warning: skipping read '124' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 1182s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '125' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 1182s Read 150 alignments... 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 1182s Read 200 alignments... 1182s 130 reads; of these: 1182s 121 (93.08%) were paired; of these: 1182s 121 (100.00%) aligned concordantly 0 times 1182s 0 (0.00%) aligned concordantly exactly 1 time 1182s 0 (0.00%) aligned concordantly >1 times 1182s ---- 1182s 121 pairs aligned concordantly 0 times; of these: 1182s 0 (0.00%) aligned discordantly 1 time 1182s ---- 1182s 121 pairs aligned 0 times concordantly or discordantly; of these: 1182s 242 mates make up the pairs; of these: 1182s 226 (93.39%) aligned 0 times 1182s 2 (0.83%) aligned exactly 1 time 1182s 14 (5.79%) aligned >1 times 1182s 9 (6.92%) were unpaired; of these: 1182s 9 (100.00%) aligned 0 times 1182s 0 (0.00%) aligned exactly 1 time 1182s 0 (0.00%) aligned >1 times 1182s 6.37% overall alignment rate 1182s Read 250 alignments... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GT 1182s GT 1182s Processing line... 1182s GT 1182s GT 1182s Processing line... 1182s GT 1182s GT 1182s Processing line... 1182s GT 1182s GT 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s AGAACACGAGCCTGTCACATCGAGA 1182s AGAACACGAGCCTGTCACATCGAGA 1182s Processing line... 1182s AGAACACGAGCCTGTCACATCGAGA 1182s AGAACACGAGCCTGTCACATCGAGA 1182s Processing line... 1182s AGAACACGAGCCTGTCACATCGAGA 1182s AGAACACGAGCCTGTCACATCGAGA 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s Processing line... 1182s GGA 1182s GGA 1182s Processing line... 1182s GGA 1182s GGA 1182s Processing line... 1182s GGA 1182s GGA 1182s Processing line... 1182s GGA 1182s GGA 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s ACC 1182s ACC 1182s Processing line... 1182s ACC 1182s ACC 1182s Processing line... 1182s ACC 1182s ACC 1182s Processing line... 1182s ACC 1182s ACC 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s TCGTG 1182s TCGTG 1182s Processing line... 1182s TCGTG 1182s TCGTG 1182s Processing line... 1182s TCGTG 1182s TCGTG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GAAGTG 1182s GAAGTG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GCG 1182s GCG 1182s Processing line... 1182s GCG 1182s GCG 1182s Processing line... 1182s GCG 1182s GCG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s AC 1182s AC 1182s Processing line... 1182s AC 1182s AC 1182s Processing line... 1182s AC 1182s AC 1182s Processing line... 1182s AC 1182s AC 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s ATGGAC 1182s ATGGAC 1182s Processing line... 1182s ATGGAC 1182s ATGGAC 1182s Processing line... 1182s ATGGAC 1182s ATGGAC 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GCTC 1182s GCTC 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s AA 1182s AA 1182s Processing line... 1182s AA 1182s AA 1182s Processing line... 1182s AA 1182s AA 1182s Processing line... 1182s AA 1182s AA 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s AGATGG 1182s AGATGG 1182s Processing line... 1182s AGATGG 1182s AGATGG 1182s Processing line... 1182s AGATGG 1182s AGATGG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s --- Summary --- 1182s Read 1 reference strings 1182s Checked 53 alignments, 0 edits 1182s --------------- 1182s PASSED 1182s ALSO checking that bowtie2 and bowtie2-align match up 1182s /usr/bin/bowtie2 --cp-min 4 --cp-ival 2 --mm --mp 8.86827001618359,5.35071818754591 --large-index -k 4 --np 3 --norc --trim5 6 --n-ceil 0.361332891608261,1.1444179805813 --score-min L,6.06341886538575,4.29188284408769 --gbar 1 -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1182s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '9' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1182s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '10' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1182s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 1182s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '32' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1182s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1182s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '35' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1182s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '41' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1182s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '42' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1182s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1182s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '94' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1182s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 1182s Warning: skipping mate #2 of read '97' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1182s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '111' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 1182s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '116' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 1182s Warning: skipping mate #1 of read '117' because length (1) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '117' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 1182s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '119' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 1182s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 1182s Warning: skipping read '124' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 1182s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '125' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 1182s 130 reads; of these: 1182s 121 (93.08%) were paired; of these: 1182s 121 (100.00%) aligned concordantly 0 times 1182s 0 (0.00%) aligned concordantly exactly 1 time 1182s 0 (0.00%) aligned concordantly >1 times 1182s ---- 1182s 121 pairs aligned concordantly 0 times; of these: 1182s 0 (0.00%) aligned discordantly 1 time 1182s ---- 1182s 121 pairs aligned 0 times concordantly or discordantly; of these: 1182s 242 mates make up the pairs; of these: 1182s 226 (93.39%) aligned 0 times 1182s 2 (0.83%) aligned exactly 1 time 1182s 14 (5.79%) aligned >1 times 1182s 9 (6.92%) were unpaired; of these: 1182s 9 (100.00%) aligned 0 times 1182s 0 (0.00%) aligned exactly 1 time 1182s 0 (0.00%) aligned >1 times 1182s 6.37% overall alignment rate 1182s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1182s Flattened IUPAC characters 1182s Mutating sequence Sim.pm.2 1182s Introducing 9 SNPs, 1/1 ref/read gaps, and 1 rearrangements 1182s Finished SNPs 1182s Finished ref gaps 1182s Finished read gaps 1182s Mutating sequence Sim.pm.1 1182s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1182s Finished SNPs 1182s Finished ref gaps 1182s Finished read gaps 1182s Mutated reference genome to subject genome 1182s SNPs introduced: 9 1182s Reference gaps introduced: 1 1182s Read gaps introduced: 2 1182s Rearrangements introduced: 1 1182s Created read sampler 1182s Sampling 115 reads 1182s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1182s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1182s parsing sequence Sim.pm.1... 1182s parsing sequence Sim.pm.2... 1182s Parsed 269 reference bases 1182s *** Run 98 of 100 1182s /usr/bin/bowtie2 --np 5 --score-min L,7.45782164526863,7.54836151684203 --gbar 1 --cp-min 4 --cp-ival 1 --mm -a --mp 7.90424424822478,6.45327315410982 --trim3 7 --rdg 33.0951622371044,13.9232677610022 --large-index -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1182s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1182s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1182s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1182s Warning: skipping read '27' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1182s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 1182s Warning: skipping read '31' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1182s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1182s Warning: skipping read '32' because it was < 2 characters long 1182s Read 50 alignments... 1182s Read 100 alignments... 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1182s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1182s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1182s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1182s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '48' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1182s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1182s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1182s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1182s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1182s Read 150 alignments... 1182s Read 200 alignments... 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1182s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1182s Read 250 alignments... 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1182s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 1182s Warning: skipping mate #2 of read '91' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1182s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1182s Warning: skipping read '93' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1182s Read 300 alignments... 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1182s Read 350 alignments... 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1182s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '100' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1182s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '106' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1182s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 1182s Warning: skipping mate #1 of read '107' because it was < 2 characters long 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1182s Read 400 alignments... 1182s Read 450 alignments... 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1182s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1182s 115 reads; of these: 1182s 95 (82.61%) were paired; of these: 1182s 92 (96.84%) aligned concordantly 0 times 1182s 0 (0.00%) aligned concordantly exactly 1 time 1182s 3 (3.16%) aligned concordantly >1 times 1182s ---- 1182s 92 pairs aligned concordantly 0 times; of these: 1182s 0 (0.00%) aligned discordantly 1 time 1182s ---- 1182s 92 pairs aligned 0 times concordantly or discordantly; of these: 1182s 184 mates make up the pairs; of these: 1182s 151 (82.07%) aligned 0 times 1182s 5 (2.72%) aligned exactly 1 time 1182s 28 (15.22%) aligned >1 times 1182s 20 (17.39%) were unpaired; of these: 1182s 15 (75.00%) aligned 0 times 1182s 3 (15.00%) aligned exactly 1 time 1182s 2 (10.00%) aligned >1 times 1182s 20.95% overall alignment rate 1182s Read 500 alignments... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s CTCG 1182s CTCG 1182s Processing line... 1182s CGAG 1182s CGAG 1182s Processing line... 1182s CTCG 1182s CTCG 1182s Processing line... 1182s CGAG 1182s CGAG 1182s Processing line... 1182s CTCG 1182s CTCG 1182s Processing line... 1182s CGAG 1182s CGAG 1182s Processing line... 1182s CGAG 1182s CGAG 1182s Processing line... 1182s CTCG 1182s CTCG 1182s Processing line... 1182s CGAG 1182s CGAG 1182s Processing line... 1182s CGAG 1182s CGAG 1182s Processing line... 1182s CGAG 1182s CGAG 1182s Processing line... 1182s Processing line... 1182s AGTA 1182s AGTA 1182s Processing line... 1182s AGTA 1182s AGTA 1182s Processing line... 1182s AGTA 1182s AGTA 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s CACATCGAGATGG 1182s CACATCGAGATGG 1182s Processing line... 1182s CACATCGAGATGG 1182s CACATCGAGATGG 1182s Processing line... 1182s CACATCGAGATGG 1182s CACATCGAGATGG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s CTC 1182s CTC 1182s Processing line... 1182s CTC 1182s CTC 1182s Processing line... 1182s CTC 1182s CTC 1182s Processing line... 1182s GAG 1182s GAG 1182s Processing line... 1182s GAG 1182s GAG 1182s Processing line... 1182s GAG 1182s GAG 1182s Processing line... 1182s GAG 1182s GAG 1182s Processing line... 1182s GAG 1182s GAG 1182s Processing line... 1182s GAG 1182s GAG 1182s Processing line... 1182s GAG 1182s GAG 1182s Processing line... 1182s GAG 1182s GAG 1182s Processing line... 1182s GAG 1182s GAG 1182s Processing line... 1182s GAG 1182s GAG 1182s Processing line... 1182s CTC 1182s CTC 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s CT 1182s CT 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GAACACGAGCCTGTCAC 1182s GAACACGAGCCTGTCAC 1182s Processing line... 1182s GAACACGAGCCTGTCAC 1182s GAACACGAGCCTGTCAC 1182s Processing line... 1182s GAACACGAGCCTGTCAC 1182s GAACACGAGCCTGTCAC 1182s Processing line... 1182s Processing line... 1182s GGTGAGGGTCGAGGAC 1182s GGTGAGGGTCGAGGAC 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s CC 1182s CC 1182s Processing line... 1182s GG 1182s GG 1182s Processing line... 1182s Processing line... 1182s AGGG 1182s AGGG 1182s Processing line... 1182s AGGG 1182s AGGG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GAGCCTGTCACAT 1182s GAGCCTGTCACAT 1182s Processing line... 1182s GAGCCTGTCACAT 1182s GAGCCTGTCACAT 1182s Processing line... 1182s GAGCCTGTCACAT 1182s GAGCCTGTCACAT 1182s Processing line... 1182s AGGGTCGAG 1182s AGGGTCGAG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s CCTGTCACATCGAGATG 1182s CCTGTCACATCGAGATG 1182s Processing line... 1182s CCTGTCACATCGAGATG 1182s CCTGTCACATCGAGATG 1182s Processing line... 1182s CCTGTCACATCGAGATG 1182s CCTGTCACATCGAGATG 1182s Processing line... 1182s GGTGAGGGT 1182s GGTGAGGGT 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s ACATCG 1182s ACATCG 1182s Processing line... 1182s ACATCG 1182s ACATCG 1182s Processing line... 1182s ACATCG 1182s ACATCG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GCT 1182s GCT 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s GCT 1182s GCT 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s GCT 1182s GCT 1182s Processing line... 1182s AGC 1182s AGC 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s CAGCGCG 1182s CAGCGCG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s AGCGCGTA 1182s AGCGCGTA 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s GC 1182s GC 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s ACGA 1182s ACGA 1182s Processing line... 1182s ACGA 1182s ACGA 1182s Processing line... 1182s TCGT 1182s TCGT 1182s Processing line... 1182s TCGT 1182s TCGT 1182s Processing line... 1182s ACGA 1182s ACGA 1182s Processing line... 1182s TCGT 1182s TCGT 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GAACACGAGCCTGTCAC 1182s GAACACGAGCCTGTCAC 1182s Processing line... 1182s GAACACGAGCCTGTCAC 1182s GAACACGAGCCTGTCAC 1182s Processing line... 1182s GAACACGAGCCTGTCAC 1182s GAACACGAGCCTGTCAC 1182s Processing line... 1182s Processing line... 1182s GGG 1182s GGG 1182s Processing line... 1182s GGG 1182s GGG 1182s Processing line... 1182s GGG 1182s GGG 1182s Processing line... 1182s GGG 1182s GGG 1182s Processing line... 1182s GGG 1182s GGG 1182s Processing line... 1182s GGG 1182s GGG 1182s Processing line... 1182s GGG 1182s GGG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GCCTGTCA 1182s GCCTGTCA 1182s Processing line... 1182s GCCTGTCA 1182s GCCTGTCA 1182s Processing line... 1182s GCCTGTCA 1182s GCCTGTCA 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s CGAGATGGACCACCTC 1182s CGAGATGGACCACCTC 1182s Processing line... 1182s CGAGATGGACCACCTC 1182s CGAGATGGACCACCTC 1182s Processing line... 1182s CGAGATGGACCACCTC 1182s CGAGATGGACCACCTC 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s TGTCACATCGAGATG 1182s TGTCACATCGAGATG 1182s Processing line... 1182s TGTCACATCGAGATG 1182s TGTCACATCGAGATG 1182s Processing line... 1182s TGTCACATCGAGATG 1182s TGTCACATCGAGATG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GGTA 1182s GGTA 1182s Processing line... 1182s Processing line... 1182s TCGAGATGGA 1182s TCGAGATGGA 1182s Processing line... 1182s TCGAGATGGA 1182s TCGAGATGGA 1182s Processing line... 1182s TCGAGATGGA 1182s TCGAGATGGA 1182s Processing line... 1182s ACGAGCCTG 1182s ACGAGCCTG 1182s Processing line... 1182s ACGAGCCTG 1182s ACGAGCCTG 1182s Processing line... 1182s ACGAGCCTG 1182s ACGAGCCTG 1182s Processing line... 1182s Processing line... 1182s CTG 1182s CTG 1182s Processing line... 1182s AGAACACGA 1182s AGAACACGA 1182s Processing line... 1182s CTG 1182s CTG 1182s Processing line... 1182s AGAACACGA 1182s AGAACACGA 1182s Processing line... 1182s CTG 1182s CTG 1182s Processing line... 1182s AGAACACGA 1182s AGAACACGA 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s TGGACCAC 1182s TGGACCAC 1182s Processing line... 1182s TGGACCAC 1182s TGGACCAC 1182s Processing line... 1182s TGGACCAC 1182s TGGACCAC 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s GTAGAACA 1182s GTAGAACA 1182s Processing line... 1182s ATTAG 1182s ATTAG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s TAGAACACGAGCCTGT 1182s TAGAACACGAGCCTGT 1182s Processing line... 1182s TAGAACACGAGCCTGT 1182s TAGAACACGAGCCTGT 1182s Processing line... 1182s TAGAACACGAGCCTGT 1182s TAGAACACGAGCCTGT 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GCTCGCAGCG 1182s GCTCGCAGCG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s ACCTCG 1182s ACCTCG 1182s Processing line... 1182s AG 1182s AG 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s AGAACACGA 1182s AGAACACGA 1182s Processing line... 1182s AGAACACGA 1182s AGAACACGA 1182s Processing line... 1182s AGAACACGA 1182s AGAACACGA 1182s Processing line... 1182s Processing line... 1182s GTCACAT 1182s GTCACAT 1182s Processing line... 1182s GTCACAT 1182s GTCACAT 1182s Processing line... 1182s GTCACAT 1182s GTCACAT 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GAACACG 1182s GAACACG 1182s Processing line... 1182s GAACACG 1182s GAACACG 1182s Processing line... 1182s GAACACG 1182s GAACACG 1182s Processing line... 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s TG 1182s TG 1182s Processing line... 1182s CA 1182s CA 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s ACG 1182s ACG 1182s Processing line... 1182s CGT 1182s CGT 1182s Processing line... 1182s CGT 1182s CGT 1182s Processing line... 1182s ACG 1182s ACG 1182s Processing line... 1182s CGT 1182s CGT 1182s Processing line... 1182s ACG 1182s ACG 1182s Processing line... 1182s CGT 1182s CGT 1182s Processing line... 1182s ACG 1182s ACG 1182s Processing line... 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s AT 1182s AT 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s GCTGA 1182s GCTGA 1182s Processing line... 1182s GCTGA 1182s GCTGA 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s Processing line... 1182s --- Summary --- 1182s Read 1 reference strings 1182s Checked 347 alignments, 0 edits 1182s --------------- 1182s PASSED 1182s ALSO checking that bowtie2 and bowtie2-align match up 1182s /usr/bin/bowtie2 --np 5 --score-min L,7.45782164526863,7.54836151684203 --gbar 1 --cp-min 4 --cp-ival 1 --mm -a --mp 7.90424424822478,6.45327315410982 --trim3 7 --rdg 33.0951622371044,13.9232677610022 --large-index -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1183s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1183s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1183s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1183s Warning: skipping read '27' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1183s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 1183s Warning: skipping read '31' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1183s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1183s Warning: skipping read '32' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1183s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1183s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1183s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1183s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '48' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1183s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1183s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1183s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1183s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1183s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1183s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 1183s Warning: skipping mate #2 of read '91' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1183s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1183s Warning: skipping read '93' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1183s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '100' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1183s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '106' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1183s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '107' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1183s 115 reads; of these: 1183s 95 (82.61%) were paired; of these: 1183s 92 (96.84%) aligned concordantly 0 times 1183s 0 (0.00%) aligned concordantly exactly 1 time 1183s 3 (3.16%) aligned concordantly >1 times 1183s ---- 1183s 92 pairs aligned concordantly 0 times; of these: 1183s 0 (0.00%) aligned discordantly 1 time 1183s ---- 1183s 92 pairs aligned 0 times concordantly or discordantly; of these: 1183s 184 mates make up the pairs; of these: 1183s 151 (82.07%) aligned 0 times 1183s 5 (2.72%) aligned exactly 1 time 1183s 28 (15.22%) aligned >1 times 1183s 20 (17.39%) were unpaired; of these: 1183s 15 (75.00%) aligned 0 times 1183s 3 (15.00%) aligned exactly 1 time 1183s 2 (10.00%) aligned >1 times 1183s 20.95% overall alignment rate 1183s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1183s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1183s /usr/bin/bowtie2 --np 5 --score-min L,7.45782164526863,7.54836151684203 --gbar 1 --cp-min 4 --cp-ival 1 --mm -a --mp 7.90424424822478,6.45327315410982 --trim3 7 --rdg 33.0951622371044,13.9232677610022 --large-index -r -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1183s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 1183s Warning: skipping read '32' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 1183s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '34' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 1183s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '48' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 1183s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '13' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 1183s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '24' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1183s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 1183s Warning: skipping read '27' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 1183s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '39' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 1183s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '40' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 1183s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '66' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1183s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 1183s Warning: skipping read '31' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 1183s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '53' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 1183s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '55' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 1183s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '100' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 1183s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '84' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 1183s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '60' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 1183s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 1183s Warning: skipping mate #2 of read '91' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1183s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 1183s Warning: skipping read '93' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 1183s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '106' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 1183s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 1183s Warning: skipping mate #1 of read '107' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 1183s 115 reads; of these: 1183s 95 (82.61%) were paired; of these: 1183s 92 (96.84%) aligned concordantly 0 times 1183s 0 (0.00%) aligned concordantly exactly 1 time 1183s 3 (3.16%) aligned concordantly >1 times 1183s ---- 1183s 92 pairs aligned concordantly 0 times; of these: 1183s 0 (0.00%) aligned discordantly 1 time 1183s ---- 1183s 92 pairs aligned 0 times concordantly or discordantly; of these: 1183s 184 mates make up the pairs; of these: 1183s 151 (82.07%) aligned 0 times 1183s 5 (2.72%) aligned exactly 1 time 1183s 28 (15.22%) aligned >1 times 1183s 20 (17.39%) were unpaired; of these: 1183s 15 (75.00%) aligned 0 times 1183s 3 (15.00%) aligned exactly 1 time 1183s 2 (10.00%) aligned >1 times 1183s 20.95% overall alignment rate 1183s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1183s Flattened IUPAC characters 1183s Mutating sequence Sim.pm.1 1183s Introducing 2 SNPs, 0/0 ref/read gaps, and 2 rearrangements 1183s Finished SNPs 1183s Finished ref gaps 1183s Finished read gaps 1183s Mutating sequence Sim.pm.2 1183s Introducing 29 SNPs, 1/0 ref/read gaps, and 0 rearrangements 1183s Finished SNPs 1183s Finished ref gaps 1183s Finished read gaps 1183s Mutated reference genome to subject genome 1183s SNPs introduced: 31 1183s Reference gaps introduced: 1 1183s Read gaps introduced: 0 1183s Rearrangements introduced: 2 1183s Created read sampler 1183s Sampling 105 reads 1183s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.fasta & /tmp/Sim.pm.4OZZSEW9_2.fasta 1183s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1183s parsing sequence Sim.pm.1... 1183s parsing sequence Sim.pm.2... 1183s Parsed 269 reference bases 1183s *** Run 99 of 100 1183s /usr/bin/bowtie2 --score-min L,2.03929636782975,2.89307632106891 --large-index --np 3 --norc --cp-min 2 --cp-ival 3 -D 6 --mm -f -x /tmp/Sim.pm.4OZZSEW9 /tmp/Sim.pm.4OZZSEW9_1.fasta 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1183s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 1183s Warning: skipping read '70' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1183s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 1183s Warning: skipping read '99' because it was < 2 characters long 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1183s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1183s 105 reads; of these: 1183s 105 (100.00%) were unpaired; of these: 1183s 89 (84.76%) aligned 0 times 1183s 4 (3.81%) aligned exactly 1 time 1183s 12 (11.43%) aligned >1 times 1183s 15.24% overall alignment rate 1183s Read 50 alignments... 1183s Read 100 alignments... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s TC 1183s TC 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s CTG 1183s CTG 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s GTGAGGGTCG 1183s GTGAGGGTCG 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s GAC 1183s GAC 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s AATTAGAGCTCGCAGCGCGT 1183s AATTAGAGCTCGCAGCGCGT 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s AGTAGAAC 1183s AGTAGAAC 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s CG 1183s CG 1183s Processing line... 1183s Processing line... 1183s GATAACCAAA 1183s GATAACCAAA 1183s Processing line... 1183s TCGTG 1183s TCGTG 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s AGTAGAAC 1183s AGTAGAAC 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s TATC 1183s TATC 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s TCACAT 1183s TCACAT 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s AGATGGA 1183s AGATGGA 1183s Processing line... 1183s Processing line... 1183s CTG 1183s CTG 1183s Processing line... 1183s ATGGACCACCTC 1183s ATGGACCACCTC 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s CTGTCACATCG 1183s CTGTCACATCG 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s Processing line... 1183s --- Summary --- 1183s Read 1 reference strings 1183s Checked 16 alignments, 0 edits 1183s --------------- 1183s PASSED 1183s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 1183s /usr/bin/bowtie2 --score-min L,2.03929636782975,2.89307632106891 --large-index --np 3 --norc --cp-min 2 --cp-ival 3 -D 6 --mm -f -p 4 -x /tmp/Sim.pm.4OZZSEW9 --reorder /tmp/Sim.pm.4OZZSEW9_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.reord.als 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 1184s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 1184s Warning: skipping read '99' because it was < 2 characters long 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 1184s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 1184s Warning: skipping read '70' because it was < 2 characters long 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 1184s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 1184s 105 reads; of these: 1184s 105 (100.00%) were unpaired; of these: 1184s 89 (84.76%) aligned 0 times 1184s 4 (3.81%) aligned exactly 1 time 1184s 12 (11.43%) aligned >1 times 1184s 15.24% overall alignment rate 1184s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als /tmp/Sim.pm.4OZZSEW9.px.reord.als 1184s Flattened IUPAC characters 1184s Mutating sequence Sim.pm.2 1184s Introducing 10 SNPs, 0/1 ref/read gaps, and 0 rearrangements 1184s Finished SNPs 1184s Finished ref gaps 1184s Finished read gaps 1184s Mutating sequence Sim.pm.1 1184s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 1184s Finished SNPs 1184s Finished ref gaps 1184s Finished read gaps 1184s Mutated reference genome to subject genome 1184s SNPs introduced: 20 1184s Reference gaps introduced: 0 1184s Read gaps introduced: 1 1184s Rearrangements introduced: 1 1184s Created read sampler 1184s Sampling 84 reads 1184s Dumping reads to temporary files /tmp/Sim.pm.4OZZSEW9_1.raw & /tmp/Sim.pm.4OZZSEW9_2.raw 1184s Parsing FASTA file /tmp/Sim.pm.4OZZSEW9.fa... 1184s *** Run 100 of 100 1184s /usr/bin/bowtie2 --np 1 --cp-min 4 --cp-ival 1 --mm --local --trim3 3 --score-min L,9.72133192946819,8.51363068570318 --gbar 1 --large-index -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw 1184s parsing sequence Sim.pm.1... 1184s parsing sequence Sim.pm.2... 1184s Parsed 269 reference bases 1185s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1185s /usr/bin/bowtie2 --np 1 --cp-min 4 --cp-ival 1 --mm --local --trim3 3 --score-min L,9.72133192946819,8.51363068570318 --gbar 1 --large-index -r -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.als 1185s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1185s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 1185s Warning: skipping mate #2 of read '29' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1185s Read 50 alignments... 1185s Warning: skipping mate #1 of read '73' because length (1) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '77' because it was < 2 characters long 1185s 84 reads; of these: 1185s 82 (97.62%) were paired; of these: 1185s 82 (100.00%) aligned concordantly 0 times 1185s 0 (0.00%) aligned concordantly exactly 1 time 1185s 0 (0.00%) aligned concordantly >1 times 1185s ---- 1185s 82 pairs aligned concordantly 0 times; of these: 1185s 0 (0.00%) aligned discordantly 1 time 1185s ---- 1185s 82 pairs aligned 0 times concordantly or discordantly; of these: 1185s 164 mates make up the pairs; of these: 1185s 164 (100.00%) aligned 0 times 1185s 0 (0.00%) aligned exactly 1 time 1185s 0 (0.00%) aligned >1 times 1185s 2 (2.38%) were unpaired; of these: 1185s 2 (100.00%) aligned 0 times 1185s 0 (0.00%) aligned exactly 1 time 1185s 0 (0.00%) aligned >1 times 1185s 0.00% overall alignment rate 1185s Read 100 alignments... 1185s Read 150 alignments... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s Processing line... 1185s --- Summary --- 1185s Read 1 reference strings 1185s Checked 0 alignments, 0 edits 1185s --------------- 1185s PASSED 1185s ALSO checking that bowtie2 and bowtie2-align match up 1185s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1185s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 1185s Warning: skipping mate #2 of read '29' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '73' because length (1) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '77' because it was < 2 characters long 1185s 84 reads; of these: 1185s 82 (97.62%) were paired; of these: 1185s 82 (100.00%) aligned concordantly 0 times 1185s 0 (0.00%) aligned concordantly exactly 1 time 1185s 0 (0.00%) aligned concordantly >1 times 1185s ---- 1185s 82 pairs aligned concordantly 0 times; of these: 1185s 0 (0.00%) aligned discordantly 1 time 1185s ---- 1185s 82 pairs aligned 0 times concordantly or discordantly; of these: 1185s 164 mates make up the pairs; of these: 1185s 164 (100.00%) aligned 0 times 1185s 0 (0.00%) aligned exactly 1 time 1185s 0 (0.00%) aligned >1 times 1185s 2 (2.38%) were unpaired; of these: 1185s 2 (100.00%) aligned 0 times 1185s 0 (0.00%) aligned exactly 1 time 1185s 0 (0.00%) aligned >1 times 1185s 0.00% overall alignment rate 1185s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 1185s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '8' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '23' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '27' because it was < 2 characters long 1185s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 1185s Warning: skipping mate #2 of read '29' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '30' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '73' because length (1) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '73' because it was < 2 characters long 1185s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 1185s Warning: skipping mate #1 of read '77' because it was < 2 characters long 1185s 84 reads; of these: 1185s 82 (97.62%) were paired; of these: 1185s 82 (100.00%) aligned concordantly 0 times 1185s 0 (0.00%) aligned concordantly exactly 1 time 1185s 0 (0.00%) aligned concordantly >1 times 1185s ---- 1185s 82 pairs aligned concordantly 0 times; of these: 1185s 0 (0.00%) aligned discordantly 1 time 1185s ---- 1185s 82 pairs aligned 0 times concordantly or discordantly; of these: 1185s 164 mates make up the pairs; of these: 1185s 164 (100.00%) aligned 0 times 1185s 0 (0.00%) aligned exactly 1 time 1185s 0 (0.00%) aligned >1 times 1185s 2 (2.38%) were unpaired; of these: 1185s 2 (100.00%) aligned 0 times 1185s 0 (0.00%) aligned exactly 1 time 1185s 0 (0.00%) aligned >1 times 1185s 0.00% overall alignment rate 1185s PASSED 1185s diff -uw /tmp/Sim.pm.4OZZSEW9.als /tmp/Sim.pm.4OZZSEW9.debug.als 1185s /usr/bin/bowtie2 --np 1 --cp-min 4 --cp-ival 1 --mm --local --trim3 3 --score-min L,9.72133192946819,8.51363068570318 --gbar 1 --large-index -r -p 2 -x /tmp/Sim.pm.4OZZSEW9 -1 /tmp/Sim.pm.4OZZSEW9_1.raw -2 /tmp/Sim.pm.4OZZSEW9_2.raw | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als 1185s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.px.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1185s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.4OZZSEW9.debug.als | grep -v '^@PG' > /tmp/Sim.pm.4OZZSEW9.debug.als.sorted 1185s diff -uw /tmp/Sim.pm.4OZZSEW9.debug.als.sorted /tmp/Sim.pm.4OZZSEW9.px.als.sorted 1185s SUCCESS: help message was detected! 1192s autopkgtest [17:13:39]: test run-unit-test: -----------------------] 1200s autopkgtest [17:13:47]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1200s run-unit-test PASS 1201s autopkgtest [17:13:48]: @@@@@@@@@@@@@@@@@@@@ summary 1201s run-unit-test PASS 1213s Creating nova instance adt-noble-arm64-bowtie2-20240325-165347-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240325.img (UUID fbff6e39-d9aa-49f2-b0e3-b936ee7913ab)...